Who doesn’t love a goodmystery anime? Watching all the pieces of a puzzle come together can make even the average anime viewerfeel like Sherlock Houndby 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 thebest mystery animeon the market.
Updated August 06, 2025 by Mark Sammut:TheWinter 2025 seasonhas 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.
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 Abyssis 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 Abyssis 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.
By the same author responsible forHyouka,Shoshimin: How to Become Ordinaryis 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.
An adaptation that seemed destined to never happen for the longest time,Plutois finally available to watch on Netflix, and the8-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.
Plutois 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.
A cult classic,Serial Experiments Lainis 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 asSerial Experiments Lainis 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.
Mononokenot only featuresone of the most visually stunning art styles in all of animebut 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.
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 Farceis 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.
Psycho-Passis 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-Passjuggles 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 afew revelations related to the world; however, this stretch of episodes arguably represents the anime’s peak. Basically,Psycho-Passshould be watched by everyone, regardless if they are craving a mystery or not.
Bungo Stray Dogsis 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 Dogsis comfortably one of thebest seinen animeever.
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 Dogsis 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.
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 aboutBaccano!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.
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-shileads 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 othermystery anime,Mushi-shimoves 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.
