25+ Of The Greatest Mystery Anime Series Worth Their Salt

mystery anime series
Written by Theo J Ellis

Mystery anime series never fail to make you curious, keep you guessing, or wanting more.

That’s just the nature of being mysterious and aloof.

These anime come in all shapes and sizes:

  • Horror
  • Action
  • Supernatural
  • Adventure
  • Comedy
  • School
  • Psychological

And plenty more.

Let’s get into it.


1. Hyouka

Hyouka episode 1

Hyouka is one of the most popular mystery series in anime.

It’s in a school setting.

On the surface this anime seems stale and basic, but it’s more than that once you get into it.

Oreki, a lazy student, is smart but doesn’t make as much effort as he could. Eru Chitanda is a curious girl with an imagination.

When they become friends, they pass the time in school by solving mysteries and doing mini investigations together. Along with 2 more support characters.

It’s one of Kyoto Animation’s best and more unique series in their catalog.

Relevant: 10+ Of The Best Anime Like Hyouka With Mysteries And More!


2. Bungou Stray Dogs

Bungou Stray Dogs 3 characters

Bungou Stray Dogs, an anime by studio bones, is about the armed detective agency. It’s basically a bunch of nut jobs with supernatural abilities.

Except one character. His name is Atsushi Nakajima. While he has powers, he’s the most “normal” and not so confident of the group.

Being an orphan is his backstory.

A common theme in this series is gangs, turf wars, and of course, the agency doing what they can to help people across the city.

You won’t find a group of diverse characters as strange, but likable as you do in Bungou Stray Dogs.


3. Zetsuen No Tempest

zetsuen no tempest aika yoshino

Zetsuen No Tempest is an anime with a poetic style to it. It might make some cringe, but the anime is stellar overall.

Also by Studio Bones, this anime is about Aika Fuwa, the younger sister of Mahiro who was murdered.

Mahiro makes it his mission to find Aika’s killer, and get revenge. He’s assisted by Yoshino, who also knew of Aika.

The third main character is Kusaribe Hakaze, the most powerful mage in the series.

The music in this anime is special. It has plenty of instruments and is played really well and fits the right scenes.

It’s an underrated series.


4. Ergo Proxy

Ergo Proxy eyes beautiful e1621879087837

Ergo Proxy is about a girl called Re-l Mayer. I’d say she’s one of the best looking female characters out there.

Her design is aesthetic, and there’s few if any direct comparisons. So they did a solid job there.

The plot is about the city of Romdo, and the mysteries behind it that start to come to light.

It’ snot the most action packed or stylish series for its action, but it is a “deep” thinking type of anime. It may not be for everyone.

Related: 31+ Of The Most Dark Anime Series That Will Shock You


5. Detective Conan

Detective Conan franchise protagonist

Detective Conan is all in the name. The anime has been running for longer than most can even claim.

1000+ episodes with ease.

With so many episodes to get through, plus movies and an endless amount of mysteries, this anime will have your hands full.

It’s only recommended to watch if you’re ready to make a serious commitment, but either way it’s a relevant series to mention here.


6. No.6

No.6 episode 7

No.6 is about 2 male characters who go on the run together. It’s not strictly Yaoi but there is some vibes here.

This anime is also by studio bones, and has tons of mystery that’s revealed bit by bit.

If you’re into Psycho Pass, Terror In Resonance or Banana Fish, this is right up your alley.

Relevant: 13+ Of The Greatest Yaoi Anime You Should Start Getting Into


7. The Garden Of Sinners

The Garden Of Sinners shiki eyes

The Garden Of Sinners is a part of the FATE universe. So in true fashion, it can be confusing at first.

The anime is about Shiki Ryogi, and all the strange events surrounding her, or characters like Touka in this fantasy/action series.

How this series works is the episodes aren’t linear. Things don’t connect episode to episode, but that’s part of its mysterious nature.

It’s not until you get through it that you can start to connect the dots.

Definitely one of the best mystery series there is, especially for its music and animation quality.


8. GoSick

GoSick series 3 characters

GoSick is about a blonde haired Loli called Victorique.

She’s a bit of a genius. You can think of it like a Death Note style of smarts, or Code Geass.

The main difference is this anime is about solving cases, be it murder or something else. And Victorique is the brains behind cracking each case.

She’s assisted by a male character.

It’s not an anime you’ll hear about much but it’s decent.


9. Kakegurui

Kakegurui funny moments

Kakegurui is all about gambling. Plain and simple. The main character: Yumeko Jabami is a bit of a gambling nut.

She gambles and takes big risks without much thought. It’s not that she isn’t prepared or witty, but more that she likes the thrill of danger.

This is part of what makes the mystery and the plot entertaining. You see it with some other characters.

Mainly female.

The main male character brings sanity to the craziness that’s happening as the series progresses.


10. Electromagnetic Girlfriend

Electromagnetic Girlfriend ova

Electromagnetic Girlfriend is a short series about Ami and Juuzawa. They witness crazy events involving barbaric murders and disturbed crimes.

Initially Ami follows Juuzawa to the point of being a nuisance, but something is revealed later.

It’s a psychological series as well as a mystery series.

By the end of the anime it all starts to make more sense as to what’s happening, why, and you can connect the dots better.

In this way, it’s a lot like Garden Of Sinners.


11. Ef: A Tale Of Memories

Ef A Tale Of Memories chihiro blush

Ef: A Tale Of Memories is a romance series few talk about. It’s more like a less popular version of Clannad.

It’s about a girl (Chihiro) with an eye patch. Every 24 hours she loses her memories and so she keeps a journal to keep track.

Just as it sounds, the anime runs deep and that’s a running theme from start to finish.

There’s 2 seasons in total, and gets compared to shows like Clannad.

Related: 26+ Of The Best Romance Anime


12. Ryuugajou Nanana

Ryuugajou Nanana episode 1

Ryuugajou Nanana is about Nana’s treasure.

Nana is one of the main characters, and before she died she went on wild adventures.

Dungeons, labyrinths, the whole lot. And she collected tons of treasures.

Now that she’s a ghost binded to a apartment, the other MC Ryuugajou takes her place with his own group.

You get action, supernatural, comedy and a variety of characters that adds to the chemistry.


13. The Melancholy Of Haruhi Suzumiya

The Melancholy Of Haruhi Suzumiya 2006

The Melancholy Of Haruhi Suzumiya is one of the popular mystery series of all time.

It’s by Kyoto Animation. At this point it’s a classic.

The anime’s about Haruhi, a protagonist who’s demanding and bossy. And the group she leads by “forcing” others to join.

As you get through it you start to see how strange, odd, and unpredictable this anime is. It gets weirder.

There is a charm to how its written, and it’s definitely one of Kyoto Animation’s oddball series.


14. Sunday Without God

Sunday Without God episode 11

Sunday Without God is a light novel adaptation, done by Madhouse Studios.

The anime is about God abandoning the world on Sunday, and the repercussions it has on society at large.

There’s a certain type of person called a grave digger. Their purpose is to help the dead pass on (they’re the living dead after God abandons the world).

Being the religious, unique anime it is, its thought provoking and touches on topics that will make you question things.


15. Terror In Resonance

Terror In Resonance 2014

Terror In Resonance starts off with a focus on terrorism. That’s clear from the first episodes highlights and what goes down.

As you get deeper into the series, you start to see it’s more than just so called terrorism. There’s a purpose to it.

It gets dark later when backstories are revealed, and more I won’t say to avoid spoilers.

It has 3 main characters who are the focus of what goes on.

Post: 13+ Mysterious Anime Characters Who Will Keep You Guessing


16. Hell Girl

Hell Girl ai enma black butterfly

Hell Girl is about Ai Enma, a girl who was once pure, turned evil after her village tries to kill her, not to mention all the hatred built up from being treated like an outcast in childhood.

She’s then punished by the Hell Master, and forced to become his slave for 100s of years.

The leads to the present story where ordinary people are:

  • Being bullied
  • Abused
  • Harassed

And basically who are made victims.

If they write down the persons name who did them wrong at 12AM, the Hell Girl is summoned. Who then sends the perpetrators to hell.

Post: 15+ Interesting Anime Girls Who Are Introverts


17. Death Note

Death Note image l lawliet

Death Note is forever a classic. It’ll never stop being talked about for years to come, even though it ended so long ago.

Made by Madhouse Studios, Death Note is about a teenager with a complex after he gets his hands on the death note.

He develops a false sense of justice and righteousness when he’s able to “judge” and kill anyone he see’s as a bad person.

I waited years to watch this and I don’t regret it. If you haven’t seen it yet, give it a go.


18. Beautiful Bones

Beautiful Bones moments

Beautiful Bones is an anime about a woman who’s an Osteologist. A person who studies the science of bones.

She’s a bit wacky, odd, but interesting and there’s never a dull moment with her curious personality.

The MAIN male character brings sanity to the mix, as he’s a little more “normal” of sorts.

Similar to some anime on this list, you won’t find a direct comparison. And it’s a lot better than it sounds.


19. Ghost Hunt

Ghost Hunt 3 characters

Ghost Hunt is a series by J.C Staff. Mai Taniyama ends up working for a company specializing in hunting and exorcising ghosts.

This later becomes a group with people like mediums, psychics, professionals, Monks, and so on who help out.

Being a horror series as well as mystery, it makes the JUMPY moments more anxious and creepy.

There’s not many Ghost series as it is, and it’s decent.

Read: A Stellar List Of 13+ Anime By J.C Staff!


20. Paprika

Paprika anime girl

Paprika is another series by Madhouse Studios. It’s one of their strangest. In fact most people will be confused watching this anime movie.

It’s about Paprika,a woman with red hair. Except that’s really not true because there’s a twist.

One thing that’s certain is the device that allows doctors to “enter” people’s dreams. And this is an important factor in the story.

If you wanna know what getting high out of your face looks like, Paprika is basically the animated version of that.

It’s nuts.

Read: The Weirdest Anime You Might Not Be Able To Take Seriously


21. Monogatari

monogatari araragi and kanbaru

Monogatari is an anime that doesn’t follow a standard plot. It’s unpredictable, odd at times, and full of mystery. Clues are littered across almost every episode.

Senjougahara Hitagi is the main female character, who can be classed as a Yandere with some sanity to her character.

Araragi Koyomi is the main male character, who builds interesting relationships with a set of girls. But not in the Harem way you’d expect.

In total there’s around 6 seasons. Start with Bakemonogatari, and get a taste to see if you’re into it or not.

If you do like it, you’ll never be able to turn back. It’s an anomaly.


22. Made In Abyss

Made In Abyss riko robot

Made In Abyss is alike a child version of Madoka Magica. “Child” meaning children for main characters.

In this adventure there’s a deep abyss that seems to go on forever. And people travel down it to find out its secrets.

Riko, one of the MC’S, has a potty mouth and a dangerous amount of curiosity. She’s helped by a robot kid.

The anime is dressed up as cute and fun, but it’s anything but that as the episodes pass by.


23. Land Of The Lustrous

Land Of The Lustrous cinnabar and phos beautiful

Land Of The Lustrous is about Lunarians. Aliens who target GEMS and kill them if necessary. Gems are the main focus of the series.

The lead character is Phos, a rebel who doesn’t like rules and cant help doing what she wants and causing trouble.

As the Gems constantly try to defend themselves against the Lunarians, other secrets and mysteries are revealed down the line.

Read: 17 Anime With Some Of The Most Beautiful Aesthetics


24. Monster

monster anime kenzo blue shirt

Monster is a horror/psychological series, with mystery elements to it. It’s about a child who’s saved through surgery to remove a bullet wound.

10 years later that same kid has become a serial killer, and Kenzo Tenma, the surgeon, regrets his decision. And finds a way to make amends.

One way is by hunting down the serial killer and killing the man himself.

The 2000’s is full of strategic, clever anime series. And Monster is one of them (just like Code Geass or Death Note).


25. Higurashi: When They Cry

YouTube video

Higurashi When They Cry is also a horror series with psychological/mystery elements to it.

The plot changes a lot, so it doesn’t follow a typical pattern.

One thing that’s consistent is Hinamizawa, the village, and the curse of the demon Oyashiro.

People seemingly end up dead for unknown reasons. Chopped up like mince meat, dead by the river, and all sorts of savagery.

Each relevant character is ultimately tested, and you get to see different shades of them when put in different situations.


26. Children Of The Whales

children of the whales episode 5

Children Of The Whales is about a moving island that’s actually a mud whale. And the people who live on it with their own society.

They’re attacked, forced to defend themselves, but are ultimately caught off guard.

There are other mysteries in the background that are slowly rising to the surface, with all the chaos going on.

The series was originally adapted from a light novel, and was done by J.C Staff.


Honorable Mentions:

  • Blood+
  • Heavens Memo Pad
  • Mirai Nikki
  • Revolutionary Girl Utena
  • Princess Principal
  • Yamada Kun And The Seven Witches
  • Penguindrum
  • Black Butler
  • Umineko: When They Cry
  • Erased
  • Mushishi
  • Darker Than Black
  • Haibane Renmei
  • Death Parade
  • Danganronpa
  • Black Bullet


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