Top 31 Best Mystery Anime

Mononoke

Mononoke is a spin-off of the Bakeneko story arc of Ayakashi: Japanese Classic Horror. It follows the Medicine Seller as he deals with various spirits or "Mononoke" in feudal Japan. Just like in the Bakeneko story, he combats with a series of tools and his vast knowledge of the supernatural on his side, but can only slay the Mononoke when he uncovers its form , the truth behind its appearance and the reason for its unusual behavior .

Mirai Nikki

This psychological thriller, based on the manga written and illustrated by Sakae Esuno, is about Yuki, a loner who's not very good with people. He prefers to write a diary on his cell phone and talk to his imaginary friend, Deus Ex Machina – The God of Time and Space. However, Yuki soon learns that Deus is more than a figment of his imagination when he makes Yuki participate in a battle royale with eleven others. The contestants are given special diaries that can predict the future, each diary possessing unique features that give it both advantages and disadvantages. Within the next 90 days, the contestants must try to survive until there is only one left standing. The winner will become the new God of Time and Space.

Shiki

During a fiercely hot summer in Sotoba, a peaceful and quiet village with a population of 1300 people, a series of bizarre deaths begin to occur. At the same time, a strange family moves into a long abandoned mansion in the region. After supposedly visiting this strange family, the fashionable Shimizu Megumi goes missing and the entire village goes out in search for her.

Bungou Stray Dogs

Stalked by a beastly white tiger, Atsushi Nakajima has no idea that the menace lives inside him—a power that catches the attention of the Armed Detective Agency. Using inhuman abilities to combat crime, this team takes Atsushi under the wing of their most eccentric member, Dazai. Together, they tear through mafia-muddled mysteries while enemies keep an eye on the tiger’s lofty bounty.

Shinsekai yori

Following a sudden outbreak of psychokinesis in 0.1% of the population, a rapid transformation swept the world. The godlike ability to manipulate matter remotely turned many power wielders to violence, inciting a long period of upheaval. Finally, after a chaotic era shaped by the rise and fall of oppressive regimes, the psychic humans were able to achieve a fragile peace by isolating their society, creating a new world bound by complex rules. In the town of Kamisu 66, 12-year-old Saki Watanabe has just awakened to her powers and is relieved to rejoin her friends—the mischievous Satoru Asahina, the shy Mamoru Itou, the cheerful Maria Akizuki, and Shun Aonuma, a mysterious boy whom Saki admires—at Sage Academy, a special school for psychics. However, unease looms as Saki begins to question the fate of those unable to awaken to their powers, and the children begin to get involved with secretive matters such as the rumored Tainted Cats said to abduct children. Shinsekai yori tells the unique coming-of-age story of Saki and her friends as they journey to grow into their roles in the supposed utopia. Accepting these roles, however, might not come easy when faced with the dark and shocking truths of society, and the impending havoc born from the new world.

Another

When Kouichi Sakakibara transfers to a new school, he senses a frightening atmosphere in his new class, a secret none of them will talk about. At the center is the beautiful Mei Misaki. Kouichi is immediately drawn to her mysterious aura, but he begins to realize that no one else in the class is aware of her presence. Soon after his arrival, what is known as the Calamity begins, and it claims the lives of many students.

Yakusoku no Neverland

Emma, Norman and Ray are the brightest kids at the Grace Field House orphanage. And under the care of the woman they refer to as “Mom,” all the kids have enjoyed a comfortable life. Good food, clean clothes and the perfect environment to learn—what more could an orphan ask for? One day, though, Emma and Norman uncover the dark truth of the outside world they are forbidden from seeing.

DEATH NOTE (Trailer)

Light Yagami is a genius high school student who is about to learn about life through a book of death. When a bored shinigami, a God of Death, named Ryuk drops a black notepad called a Death Note, Light receives power over life and death with the stroke of a pen. Determined to use this dark gift for the best, Light sets out to rid the world of evil… namely, the people he believes to be evil. Should anyone hold such power? The consequences of Light’s actions will set the world ablaze.

Kara no Kyoukai: Shuushou

Subete ga F ni Naru: THE PERFECT INSIDER

The story of the original Subete ga F ni Naru novel revolves around Souhei Saikawa, a member of the Saikawa Research Lab. He goes on a vacation held by the lab, and Moe Nishinosono, the daughter of his mentor, joins the group on their vacation despite not being a part of the lab. There, the two end up finding a corpse. The two work together to solve the mysteries of what becomes a serial murder case.

serial experiments lain

Lain Iwakura appears to be an ordinary girl, with almost no experience with computers. Yet the sudden suicide of a schoolmate combined with a number of strange occurrences conspire to pull Lain into the world of the Wired, where she gradually learns that nothing is what it seems to be... not even Lain herself.

Bakemonogatari

First season of the Monogatari Series, part 1/6. Contains the arcs Hitagi Crab, Mayoi Snail, Suruga Monkey, Nadeko Snake, and Tsubasa Cat from the Bakemonogatari light novels. Thanks to Meme Oshino, Koyomi Araragi, a high school student, is able to remain a human after coming across a female vampire... However, since the incident, Koyomi seems to meet girls who have an apparition-related issue. Hitagi Senjyogahara doesn’t weigh anything, Suruga Kanbaru’s right arm becomes like that of a monkey’s, and a young girl, Mayoi, cannot find her way home no matter how many times she tries. Koyomi, a Mr. Nice Guy, ends up helping each and every girl solve her problem with the help of Meme Oshino.

Mushishi (Trailer)

They are neither plants nor animals. They differ from other forms of life such as the micro-organisms and the fungi. Instead they resemble the primeval body of life and are generally known as "Mushi". Their existence and appearance are unknown to many and only a limited number of humans are aware of them. Ginko is a "Mushi-shi" who travels around to investigate and find out more about the "Mushi". In the process, he also lends a helping hand to people who face problems with supernatural occurances which may be related to the "Mushi".

Kubikiri Cycle: Aoiro Savant to Zaregotozukai

It's the vacation of a lifetime, a trip to a remote island filled with geniuses–and murder. On Wet Crow's Feather Island, a tiny speck in the Sea of Japan, lives Akagami Iria, the exiled daughter of a powerful family. Born into great wealth, she was a princess of the highest pedigree–until she was cut off by the leader of the Akagami Foundation. For the last five years, she's lived on Feather Island with her maids. But she hasn't been alone. She has invited the best minds Japan has to offer to come and stay with her. And so nineteen-year-old college student Ii-chan and his best friend, computer genius Kunagisa Tomo, find themselves as Iria’s guests at her elaborate mansion. Surrounded by fascinating women – a chef, a fortune-teller, a scholar, and an artist, not to mention his own friend Tomo – Ii-chan is feeling a little overmatched intellectually. But the sudden discovery of a grisly murder sends the island into shock. And Ii-chan discovers that he does possess a bit of genius: the ability to discover what is real and what is fake, who is who they claim to be and who is a killer.

ID: INVADED

Welcome to Kura, an organization that investigates crime using the Mizuhanome system which senses the drive to kill. Sakaido is a brilliant detective and pilot of the Mizuhanome. To solve a case, he enters the world of the killer's unconscious mind: the id well. In the shadows of brutal and puzzling cases lurks John Walker, the Serial Killer Creator. Where will Sakaido's pursuit lead?

Owarimonogatari

Third season of the Monogatari Series, part 3/5. Contains the arcs Ougi Formula, Sodachi Riddle, Sodachi Lost and Shinobu Mail from the Owarimonogatari light novels. During the month of October of his third year in high school, Koyomi Araragi is introduced to a transfer student named Ougi Oshino by his underclassman Suruga Kanbaru. Ougi tells Koyomi that she has something she wishes to consult with him. When she draws the map of Naoetsu High School, she finds something peculiar on there. This discovery reveals a tale that wasn’t meant to be told, and this makes Koyomi’s high school life totally different. This is the story that brings to light “what” makes Koyomi Araragi. This is the story that reveals the “beginning” of everything.

Baccano! (Trailer)

During the early 1930s in Chicago, the transcontinental train, Flying Pussyfoot, is starting its legendary journey that will leave a trail of blood all over the country. At the same time in New York, the ambitious scientist Szilard and his unwilling aide Ennis, are looking for missing bottles of the immortality elixir. In addition, a war between the mafia groups is getting worse. On board the Advena Avis, in 1711, alchemists are about to learn the price of immortality. Based on the award winning light novels of the same name, this anime adaptation follows several events that initially seem unrelated, both in time and place, but are part of a much bigger story—one of alchemy, survival and immortality. Merging these events together are the kindhearted would-be thieves, Isaac and Miria, connecting various people, all of them with their own hidden ambitions and agendas, and creating lifelong bonds and consequences for everyone involved.

Ergo Proxy

Something is wrong in the perfect domed city of Romdo. Between the sudden rash of murders and a virus affecting all AutoReivs-cyborg companions and workers who assist the people of Romdo - all is not right in their dome home. Detective Re-l Meyer begins to investigate, seeking answers to the weird occurrences that are happening more and more around her. But when she begins to uncover the truth, her world is turned upside down. First, the strange immigrant Vincent Law goes missing and then a monster appears before her, shaking her to her core. But this monster is something more, something dangerous and sinister. With each question and mystery, she is led back to the creature. But what is it really? What purpose does it serve? A sign of the end or a sign of a new beginning? Whatever it is, it repeatedly brings her back to Vincent and soon, alongside his journey back to another dome world called, Mosk. As they make their way across scarred and deserted Earth, Re-l and Vincent will learn more about the monster and the "awakening"-which could be more of an ending than a beginning.

Higurashi no Naku Koro ni Gou

New kid Keiichi Maebara is settling into his new home of peaceful Hinamizawa village. Making quick friends with the girls from his school, he's arrived in time for the big festival of the year. But something about this isolated town seems "off," and his feelings of dread continue to grow. With a gnawing fear that he's right, what dark secrets could this small community be hiding?

MONSTER (Trailer)

Dr. Kenzo Tenma is a renowned Japanese brain surgeon working at a leading hospital in Germany. One night, Dr. Tenma risks his reputation and career to save the life of a critically wounded young boy over that of the town mayor who had been planning to support the hospital financially. A string of mysterious murders begin to occur soon after the operation, and Dr. Tenma emerges as the primary suspect despite no incriminating evidence. A doctor is taught to believe that all life is equal; however, when another series of murders occur in the surgeon's vicinity, Dr. Tenma's beliefs are shaken as his actions that night are shown to have much broader consequences than he could have imagined. Leaving behind his life as a surgeon he embarks on a journey across the country to unravel the mystery of the boy he saved.

Mawaru Penguindrum

Once you make a decision, does the universe conspire to make it happen? Is destiny a matter of chance, a matter of choice or the complex outcome of thousands of warring strands of fate? All twins Kanba and Shoma know is that when their terminally ill sister Himari collapses at the aquarium, her death is somehow temporarily reversed by the penguin hat that she had asked for. It's a provisional resurrection, however, and it comes at a price: to keep Himari alive they need to find the mysterious Penguin Drum. In order to do that, they must first find the links to a complex interlocking chain of riddles that has wrapped around their entire existence, and unravel the knots that tie them to mystifying diary and a baffling string of strangers and semi-acquaintances who all have their own secrets, agendas and "survival strategies." And in order for Himari to live, someone else's chosen destiny will have to change. It's a story of love, fate, life, death... and Penguins!

Koukaku Kidoutai: STAND ALONE COMPLEX

In the not so distant future, mankind has advanced to a state where complete body transplants from flesh to machine is possible. This allows for great increases in both physical and cybernetic prowess and blurring the lines between the two worlds. However, criminals can also make full use of such technology, leading to new and sometimes, very dangerous crimes. In response to such innovative new methods, the Japanese Government has established Section 9, an independently operating police unit which deals with such highly sensitive crimes. Led by Daisuke Aramaki and Motoko Kusanagi, Section 9 deals with such crimes over the entire social spectrum, usually with success. However, when faced with a new A level hacker nicknamed “The Laughing Man”, the team is thrown into a dangerous cat and mouse game, following the hacker’s trail as it leaves its mark on Japan.

GOSICK

Kazuya Kujou is a foreign student at Saint Marguerite Academy, a luxurious boarding school in the Southern European country of Sauville. Originally from Japan, his jet-black hair and dark brown eyes cause his peers to shun him and give him the nickname "Black Reaper," based on a popular urban legend about the traveler who brings death in the spring. On a day like any other, Kujou visits the school's extravagant library in search of ghost stories. However, his focus soon changes as he becomes curious about a golden strand of hair on the stairs. The steps lead him to a large garden and a beautiful doll-like girl known as Victorique de Blois, whose complex and imaginative foresight allows her to predict their futures, now intertwined. With more mysteries quickly developing—including the appearance of a ghost ship and an alchemist with the power of transmutation—Victorique and Kujou, bound by fate and their unique skills, have no choice but to rely on each other.

Death Parade (Trailer)

When two people die at the same time, they’re sent to a place that’s neither heaven nor hell—a lavish bar between worlds where the stakes are high and the rules are simple: if you win you live again, if you die… you’re gone for good. Decim is the bartender charged with serving the souls who enter Quindecim. He may make a mean cocktail, but his true profession is to play the role of arbiter—a judge who determines whether or not a soul is worthy of reincarnation. To aid in his judgment, the bar’s patrons are forced to play simple games laced with sadistic twists designed to bring their true natures to light. To Decim, judgment has always been black and white—that is—until he meets a mysterious young woman whose fate seems impossible to decide. His indecision shakes the very foundation of the games and raises the biggest question of all: Who is fit to judge the dead?

Boku dake ga Inai Machi

Satoru Fujinuma is a 29 year old manga artist struggling to make a name for himself following his debut. But, that was not the only thing in his life that Satoru was feeling frustrated about… He has a unique supernatural ability of being forced to prevent deaths and catastrophes by being sent back in time before the incident occurred, repeating time until the accident is prevented. One day, he gets involved in an accident that has him framed as a murderer. Desperate to save the victim, he sends himself back in time only to find himself as a grade-schooler one month before fellow classmate Kayo Hinazuki went missing. Satoru now embarks on a new quest: to save Kayo and solve the mystery behind her disappearance.

Houseki no Kuni

In the mysterious future, crystalline organisms called Gems inhabit a world that has been destroyed by six meteors. Each Gem is assigned a role in order to fight against the Lunarians, a species who attacks them in order to shatter their bodies and use them as decorations. Phosphophyllite, also known as Phos, is a young and fragile Gem who dreams of helping their friends in the war effort. Instead, they are told to compile an encyclopedia because of their delicate condition. After begrudgingly embarking on this task, Phos meets Cinnabar, an intelligent gem who has been relegated to patrolling the isolated island at night because of the corrosive poison their body creates. After seeing how unhappy Cinnabar is, Phos decides to find a role that both of the rejected Gems can enjoy. Houseki no Kuni follows Phos' efforts to be useful and protect their fellow Gems.

Gankutsuou

Gankutsuou is an anime loosely based on the novel The Count of Monte Cristo by Alexandre Dumas. It tells the story of Albert Morcerf, a young aristocrat who happens to befriend a wealthy nobleman, The Count of Monte Cristo, through a series of bizarre events. Fascinated by the Count's charm, Albert invites him to meet his friends and family, all of whom happen to be part of the upper class society of Paris, France. Unfortunately, little does Albert realize that the Count has ulterior motives in mind.

Kyokou Suiri

At the young age of 11, Kotoko Iwanaga was abducted by youkai for two weeks and asked to become their "God of Wisdom," a mediator between the spirit and human worlds, to which the girl quickly agreed but at the cost of her right eye and left leg. Now, six years later, whenever youkai wish for their problems to be solved, they make their way to Kotoko for consultation. Meanwhile, Kurou Sakuragawa, a 22-year-old university student, has just broken up with his girlfriend after he fled alone when the two encountered a kappa. Seeing this as her chance to become closer with him, Kotoko immediately makes her move, hoping to get married to Kurou one day. However, she quickly realizes there is something more to Kurou. With this knowledge, she asks for his help in solving the various issues presented by the supernatural, all the while wishing her newfound partner will eventually reciprocate her feelings.

Danganronpa: Kibou no Gakuen to Zetsubou no Koukousei - The Animation

A group of 15 elite high school students are gathered at a very special, high class high school. To graduate from this high school essentially means you'll succeed in life, but graduating is very difficult. The school is presided over by a bear called Monokuma, and he explains to them that their graduation hinges around committing a murder. The only way to graduate is to kill one of your classmates and get away with it. If the other classmates discover the identity of the killer, the killer is the only one executed. However, if they fail to catch the killer, only the killer graduates and the others are annihilated. Which of the 15 will survive the bloodbath to come?

Shingeki no Kyojin (Trailer)

Several hundred years ago, humans were nearly exterminated by titans. Titans are typically several stories tall, seem to have no intelligence, devour human beings and, worst of all, seem to do it for the pleasure rather than as a food source. A small percentage of humanity survived by walling themselves in a city protected by extremely high walls, even taller than the biggest of titans. Flash forward to the present and the city has not seen a titan in over 100 years. Teenage boy Eren and his foster sister Mikasa witness something horrific as the city walls are destroyed by a colossal titan that appears out of thin air. As the smaller titans flood the city, the two kids watch in horror as their mother is eaten alive. Eren vows that he will murder every single titan and take revenge for all of mankind.

Odd Taxi (Trailer)

The taxi driver Odokawa lives a very mundane life. He has no family, doesn't really hang out with others, and he's an oddball who is narrow-minded and doesn't talk much. The only people he can call his friends are his doctor, Gouriki and his classmate from high school, Kakibana. All of his patrons seem to be slightly odd themselves. The college student who wants the world to notice him online, Kabasawa. A nurse with secrets named Shirakawa. A comedy duo that just can't catch a break named the Homosapiens. A local hoodlum named Dobu. An idol group that's just starting out named Mystery Kiss... All these mundane conversations somehow eventually lead to a girl who's gone missing.