Best Mystery Anime

Who doesn’t love a good mystery anime? Watching all the pieces of a puzzle come together can make even the average anime viewer feel like Sherlock Hound by the end of a series. Mystery plots either come in two forms — well-crafted masterpieces or sloppily constructed misadventures where the ending is far too obvious.

Fortunately, Japanese animators and storytellers seem to have a knack for tackling the genre with grace and style, weaving captivating brain-teasers with charming characters, intense drama, and even a touch of humor. Let’s take a look at the best mystery anime on the market.

Updated March 16, 2025 by Mark Sammut: The Winter 2025 season has quite a few fun mystery anime, beyond just The Apothecary Diaries’ sequel. While not quite among the genre’s best efforts ever, Tasokare Hotel and Ameku M.D. are above-average additions that could hit the mark with people who want episodic content. Conversely, they can check out some of the all-time greats.

23

Made In Abyss

MyAnimeList: 8.64 (Season 1)

When someone thinks “mystery,” they might be inclined to imagine whodunits, but those stories only make up a small part of the genre’s scope. Even if it does not feature a case that needs to be cracked, Made in Abyss is completely about the unknown. The anime follows two kids of wildly different origins as they venture down a massive dungeon known as the Abyss, a place that defies logic and explanation. Despite serving as the graveyard for many adventurers, the Abyss has a strange pull that continues to relentlessly attract new victims, many of whom are driven by a desire to uncover the location’s secrets.

Made in Abyss is dark, hauntingly beautiful, and viscerally gory. It is a surreal adventure anime that drops its characters (and audience) into a world they cannot possibly hope to comprehend.

22

Shoshimin: How to Become Ordinary

MyAnimeList: 7.29

By the same author responsible for Hyouka, Shoshimin: How to Become Ordinary is a mystery anime about (primarily) mundane cases. For instance, one episode finds the protagonists questioning how another character managed to create great hot cocoa while seemingly using fewer cups than would be required.

While hardly packed with tension, these small puzzles are nevertheless entertaining, especially since they are driven by two charismatic characters who are shrouded in mystery. The “How to Become Ordinary” subtitle refers to Yuki and Jougorou’s ongoing effort to leave behind their past selves, all in the hopes of appearing “normal” while in high school.

21

Pluto

MyAnimeList: 8.45

An adaptation that seemed destined to never happen for the longest time, Pluto is finally available to watch on Netflix, and the 8-part OVA does a great job of honoring Naoki Urasawa’s source material. A series of murders targeting humans and robots sends the world into chaos, and Gesicht is tasked with solving the case.

Pluto is a very interesting show that tackles common sci-fi themes like human identity in a novel way due to the presentation of its society. The story’s strength lies in its character exploration, particularly Gesicht and Atom. The central case is engaging, but it is not an especially strong mystery.

20

Serial Experiments Lain

MyAnimeList: 8.09

A cult classic, Serial Experiments Lain is dense, to the point that multiple viewings might be required to fully appreciate its content. Inspired by the early days of the internet, the story revolves around Lain, a lonely girl who immerses herself in a digital world after receiving a message from a recently deceased classmate. As she spends more time in The Wired, the name for the virtual world, she begins to lose touch with reality and also her own self-image.

“Mystery” might not be the best descriptor as Serial Experiments Lain is more of a psychological character study than anything else. However, the anime shrouds many of its ideas and themes in mystery, encouraging viewers to interpret and read into what they are seeing.

19

Mononoke

MyAnimeList: 8.42

Mononoke not only features one of the most visually stunning art styles in all of anime but also complex mysteries to work through in each episode. The Medicine Seller must figure out each spirit’s form, truth, and reason before being able to exorcise it with his sword.

The series really digs into the darker parts of human nature with a supernatural backdrop as humans must take terrible actions for vengeful Mononoke to exist in the first place. The revelations of the final episode will leave viewers particularly stunned, so be braced for impact when watching.

18

Undead Murder Farce

MyAnimeList: 7.86

In an alternative version of the 19th century, humans live alongside monsters, although the relationship is far from harmonious. Paid to fight creatures by a circus, Tsugaru’s purposeless life is given direction when he meets an immortal woman without a body, and the two agree to go on a journey to find the person responsible for her predicament. Along the way, they decide to take on an array of supernatural-themed cases, starting with the murder of a female vampire. Undead Murder Farce is just a delightful mystery anime.

Aya and Tsugaru have fantastic chemistry, with the former serving as the brains of the operation while the latter acts as the muscle who remarks, witty or otherwise. While the anime dedicates its opening episode to setting up the protagonists’ situations and the core mystery, the second episode immediately dives into the first case, and the show does not slow down from that point on.

17

Psycho-Pass

Brilliant Detective Sci-Fi Anime With A Few Good Mysteries

Psycho-Pass is comfortably among the best detective anime of all time, if not just straight-up the best. It is also a fantastic sci-fi series that investigates tried-and-tested themes like precognition and human will. Finally, it is a pretty good mystery anime, at least at times. Psycho-Pass juggles quite a few different genres, and crafting fine-tuned mysteries that take the audience on a ride is not always the point.

For example, the second half of season 1 does not have much of a mystery element to it, except for a few revelations related to the world; however, this stretch of episodes arguably represents the anime’s peak. Basically, Psycho-Pass should be watched by everyone, regardless if they are craving a mystery or not.

16

Bungo Stray Dogs

MyAnimeList: 7.81 (Season 1)

Bungo Stray Dogs is brilliant, but not at first. Although very popular, the anime can put off new viewers due to a fairly mediocre opening season that mostly plays out like a stylish battle shonen with literary names and supernatural powers. While hardly terrible, these 12 episodes are mediocre and mostly exist to set up the main characters, so they can feel a bit directionless at times. Fortunately, the anime starts to pick up steam during season two, paving the way for three fantastic follow-ups. By season 5, Bungo Stray Dogs is comfortably one of the best seinen anime ever.

The Armed Detective Agency takes on cases that involve supernatural abilities in some form or another, and they range from fairly small to operations that can change the entire world. Along with plenty of top-notch fight sequences, Bungo Stray Dogs is not afraid to slow things down and get cerebral, dedicating full episodes and arcs to detective-style breakdowns and mental battles. It is a blast.

15

Baccano!

MyAnimeList: 8.35

What does a group of alchemists from 1711 have to do with a transcontinental train in the 1930s? Baccano! follows several seemingly unrelated events while slowly creating a full picture of a much more expansive story. The show is perfect for fans of historical dramas who want a bit of puzzle-solving to go along with their viewing experience.

Based on a light novel that has won several awards, this adaptation is sure to entertain anyone who watches it. The main negative thing about Baccano! is that the anime only covers a very small fraction of the source material, and there is nothing to suggest that a continuation is on the cards. Consequently, while the show is definitely worth watching, it is really just an appetizer for the light novel.

14

Mushi-Shi

MyAnimeList: 8.65 (Season 1)

Ginko is a Mushishi — a person who studies the mysterious entities known as Mushi. The Mushi are almost unknowable entities that are capable of taking on basically any form and seem to lack any human concept of mortality.

Mushi-shi leads fans on Ginko’s journey as he tries to chase down any sightings of the strange creatures and tries to figure out what their existence means both physically and philosophically. Compared to other mystery anime, Mushi-shi moves at a far slower and more relaxed pace, and the show is more of a slice of life than a suspenseful thriller; nevertheless, it is great.

13

The Promised Neverland

MyAnimeList: 8.48 (Season 1)

While not a perfect adaptation of the manga, The Promised Neverland is still a perfect blending of the thriller, psychological, horror, and mystery genres.

Without giving too many spoilers, three children who live in an orphanage slowly learn that being adopted out to a family isn’t what it really seems. With well-written plot twists peppered through the episodes, The Promised Neverland is sure to leave viewers on the edge of their seats. Season 1 is especially strong, telling a well-paced story filled with suspense and mystery. The sequel is a bit more polarizing and rushed.

12

The Apothecary Diaries

MyAnimeList: 8.88 (Season 1)

The Apothecary Diaries was one of the best shows in two subsequent years (2023 and 2024). The story follows Maomao, a girl who has learned medicine through her father, as she finds herself unwillingly employed by the Imperial Palace. Initially, she wants to just stay out of trouble so she can leave as soon as possible; however, her inquisitive mind gets the better of her when she hears about a curse afflicting two babies. After solving that mystery, Maomao catches the eye of an eunuch named Jinshi, leading her to take on many different mysteries that plague the Imperial Palace.

The Apothecary Diaries regularly introduces new puzzles to test Maomao’s medical knowledge, and these cases are generally entertaining. However, the anime’s core appeal is its characters and setting rather than its mysteries, most of which are introduced and solved within the same episode without too much fuss. Maomao is a fantastic and charismatic lead who carries the story on her back, although she is generally surrounded by interesting secondary characters.

11

The Garden Of Sinners

MyAnimeList: 7.57 (Movie 1)

Based on a Type-Moon light novel, The Garden of Sinners is a challenging sit, both thematically and narratively. Consisting of eight movies and some short entries, the series revolves around a detective agency that investigates supernatural-themed cases, although that description makes this story sound much more conventional than it actually is.

Telling its story out of chronological order, The Garden of Sinners is first and foremost a character study, specifically of Shiki Ryougi. An anti-social girl who possesses the ability to see someone’s death lines, Shiki is an enigmatic and compelling figure; she is not necessarily likable, but she is deeply fascinating. The movies weave a tale of suffering, growth, and compromise. Now, it should be said that not every entry is a mesmerizing watch, particularly on initial viewing, but when the series hits the mark, The Garden of Sinners is among the best mystery anime. Paradox Spiral and A Study in Murder – Part 2 are especially strong.

10

Erased

MyAnimeList: 8.30

One of the most well-known mystery anime, Erased gets off to a flying start, and it largely succeeds in maintaining that standard for most of its run. After suffering a personal tragedy, Satoru suddenly finds himself teleported nearly two decades in the past, where he must investigate the (impending) disappearance of one of his classmates since it directly ties to his future situation.

Erased is a whodunit with a time travel twist, and the anime prioritizes its characters over telling a story packed with turns and complications (although it has those too). Tackling themes like abuse, the story covers some rather challenging ground with maturity and intelligence.

9

Orb: On the Movements of the Earth

MyAnimeList: 8.51

One of the best Fall 2024 anime, Orb: On the Movements of the Earth is captivating and singular. A historical epic that teleports viewers to Poland during the 1400s, the story chronicles a line of people who are pulled to investigate the true mechanics that govern the universe.

The church’s doctrine states that Earth is the center of everything, and challenging that belief leads to captivity, torture, and death. Despite knowing the risks, certain folks refuse to merely be told what to think, and they are willing to risk everything. While not telling a conventional whodunit mystery, Orb: On the Movements of the Earth nevertheless represents the genre at its intriguing best.

8

Ghost In The Shell: Stand Alone Complex

MyAnimeList: 8.42 (Season 1)

With Yutaka Maseba of Sailor Moon, Trigun, and Akira fame behind Stand Alone Complex, it’s no wonder it is remembered as one of the best parts of the Ghost in the Shell franchise.

The special police force at Station 9 face a lot of unique enemies but none as challenging to take down as “The Laughing Man.” Watching the team try to play a game of cat and mouse with the mysterious hacker is thrilling right through the end. Combining action, social commentary, and suspense, Stand Alone Complex is the complete package, with both seasons being fantastic.

7

Death Note

MyAnimeList: 8.62

It’s impossible to mention anime in the mystery genre without discussing this masterpiece of psychological anime. Death Note’s signature twists and turns as Light Yagami and L engage in their battle of wits are so intense that even the most seasoned detectives might have a hard time seeing them coming.

What makes the show particularly strong is the limitations placed upon its titular Death Notes making it so that Light must find clever ways to evade them without shortening his own lifespan with L hot on his trail. If even a bag of potato chips can be the ultimate psychological weapon, imagine what else the two come up with.

6

Link Click

MyAnimeList: 8.73 (Season 1)

Link Click is a Chinese donghua and not a Japanese anime, so an argument could be made that it does not qualify. However, the series is on Crunchyroll and even has a profile on MyAnimeList. More importantly, it is great enough to warrant an exception.

LAN Studio’s Link Click is a great entry point into donghua, along with just being a fantastic mystery show in general. Initially, the series will seem to follow a case-of-the-week structure, only to slowly transition into an overarching story that incorporates elements from previous episodes. The transition is well done, especially since both the cases and the continuous narrative are fascinating, emotional, and intense.

So, what is Link Click about? Well, it focuses on two guys who run a unique business that can provide closure to clients. Cheng Xiaoshi can travel to the past by using photos, allowing him to operate the body of the person who took the image. Lu Guang is his partner, and his main job is to guide Cheng while he is using this power. Together, they help people recontextualize the past to help them move forward in the present. However, they primarily exist to gather information, and Cheng should avoid changing events as much as possible. Naturally, there are consequences when he doesn’t stick to that important rule.

5

Oddtaxi

MyAnimeList: 8.65

Oddtaxi deserves to be watched by as many people as possible. The lore and mystery that unfolds throughout the series expands beyond the show itself. There are real-life Twitter accounts for characters, a hidden audio drama on YouTube, and even foreshadowing for the series finale in the official music video for the opening song.

Fans will have many opportunities to try and untangle the web of what happens in the show. Just be prepared to still guess wrong in the end.

4

Summer Time Rendering

MyAnimeList: 8.47

One of the best anime of 2022, Summer Time Rendering did not get the attention it deserved during its initial run due to not being readily available on a Western streaming service. Set on a Japanese island, the story follows Shinpei, a teenager who returns home following the death of a close childhood friend. Before long, the protagonist begins to experience unusual phenomena, and he eventually finds himself stuck in a time loop that resets whenever he is killed.

Summer Time Rendering largely sticks to Shinpei’s perspective, who is not only a likable and proactive main character but also has an analytical mind that does not venture into superhuman territory. The anime is expertly paced too, with most episodes concluding with a shocking reveal or powerful moment.