16. The Kisugi Sisters (Cat’s Eye)
TheKisugi sisters—Rui, Hitomi, and Ai—are art thieves who only steal works that once belonged to their father. They operate a cafe by day as their cover, which comes in handy for intel gathering.
By night, they shift gears and perform impossible heists. Although they always give hints as to what they’re going to steal, the police force never manages to catch them.
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15. The Guild (Bungo Stray Dogs)
The animeBungo Stray Dogsfeatures a handful of different organizations, like Port Mafia and the Armed Detective Agency. But there’s alsoThe Guild, which is similarly comprised of Gifted individuals, but this one operates as a secret society from outside Japan.
They’re quite rich because their leader comes from old money (The Great Fitzgerald), and Francis Scott Key Fitzgerald is able to enhance his physical attributes in proportion to the wealth he spent to acquire it. The higher the amount, the stronger he can be.
Other Gifted members of the group include Howard Lovecraft (who almost took on both Chuya and Dazai on his own) and Louisa May Alcott (who’s in charge of their plans and strategies).
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14. V (Tokyo Ghoul)
TheVorganization wasn’t fully explored in theTokyo Ghoulanime series, yet they played a crucial part in the development of characters and plot. They’re overseers who work in the shadows to maintain the balance between ghoul and human societies.
Members include Kisho Arima, Matsuri Washuu, Kichimura Washuu, and other unnamed characters who wear all-black outfits. Yoshimura, the manager of the Anteiku cafe, was also once a member of V, who worked as the organization’s Cleaner (dispatcher).
13. SEELE (Neon Genesis Evangelion)
While NERV is the primary agency that’s responsible for EVA operations,SEELEis the organization that’s responsible for the events ofNeon Genesis Evangelion.
They have ties with various world leaders and other world organizations, and their mission statement is to “unite humanity” using the so-called Human Instrumentality Project.
They’d been operating for many years behind the shadows, and they even helped cause the Second Impact. The incident was commonly known as some sort of accident, but in reality, it was a planned operation that almost ended in mankind’s extinction.
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12. Root (Naruto Shippuden)
The Anbu were introduced halfway through the originalNarutoanime as special ninjas who work directly under the Hokage. Much later, inNaruto Shippuden, we learned that there’s a secret branch of Anbu calledRootwho work directly for Danzo.
Root is a shady group consisting of individuals who undergo special training from childhood. They’re raised in pairs like brothers, then must fight each other to the death on the day of their graduation.
This process kills their emotional senses, crafting a true assassin that can kill without any remorse or pity on their targets, and these assassins operate in the shadows as “unseen ones who support Konoha.”
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11. Soul Society (Bleach)
Soul Societyis a special organization that remains unknown to humans because they exist beyond the human realm.
Soul Reapers exist in a world of ghosts, spirits, and Hollows. They’re all invisible to human eyes, but their existence greatly affects both realms—of the living and of the dead.
Their works include the purification of souls before they can enter Soul Society (similar to the afterlife) as well as the elimination of Hollows (monsters that eat the souls of both the deceased and the living).
Related:The Best Anime About Ghosts and Otherworldly Spirits
10. Noah’s Ark Circus (Black Butler)
Noah’s Ark Circus, as the name suggests, is a traveling circus comprised of different individuals with different skills and performances. From beast tamers to acrobats, this circus offers entertainment like no other.
But it’s just a front to cover up all the sinister activity that happens offstage—wherever this circus performs, you’ll also find numerous incidents of missing children. It all leads to some gruesome truths that even the performers aren’t totally aware of.
9. Jujutsu Sorcerers (Jujutsu Kaisen)
Sometimes, there are cases that a normal police force can’t handle, and this is especially true when there are paranormal elements involved. That’s whenJujutsu Sorcerersstep in and take over.
Even the police don’t know the full details of who they are, why they arrive on crime scenes, or how they get there even before their own forensics division does.
All they know is that Jujutsu Sorcerers investigate the inexplicable (like the misconfigured corpses left by Mahito in the theater).
To make sure their secrets don’t get out, Jujutsu Sorcerers disclose misleading details that make the incidents look like they were committed by human hands.
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8. Black Organization (Case Closed)
Black Organizationis the main antagonist of theCase Closedanime series, but they’re known only by a handful of characters.
They’re the ones responsible for Shinichi Kudo’s current situation, who was turned into a young boy by the APTX drug.
The Black Organization’s operations include assassinations and other criminal activities, which are cover-ups for their truer and more sinister motives. Their members used alcoholic beverages as codenames, like Gin, Bourbon, and Vodka.
Though they work in secrecy, law agencies have managed to infiltrate and plant double agents among their ranks.
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7. Direct Attack (Lycoris Recoil)
InLycoris Recoil,Direct Attack(orDA) is like most clandestine law enforcement agencies, except they specialize in training and employing young girls, who are known as Lycoris.
DA maintains peace and prevents crimes before they happen, usually by eliminating threats and killing targets with no one noticing.
Why work secretly when they could operate overtly like normal police organizations? Well, it’s their duty to make people believe that there are no more threats and that they’re living in a harmonious community.
Related:The Best Anime Police Officers and Cop Characters, Ranked
6. Twelve Kizuki (Demon Slayer)
InDemon Slayer, the existence of demons is a myth amongst normal people. No one has any real evidence because anyone who encounters a demon always ends up dead. Dead men tell no tales, right?
And if regular demons are mythical, then it only makes sense that the highest-ranking demons—theTwelve Kizuki—are complete unknowns to the world and the people.
These special demons have the power to stand on equal ground against the Hashira (or even surpass them) using their unique Blood Demon Arts plus the immense power they acquire from devouring humans.
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5. Shadow Garden (The Eminence in Shadow)
Cid Kagenou (a.k.a. Shadow) is the leader ofShadow Garden, a secret organization he founded out of his hero/vigilante delusion. He believes the world is secretly run by the Cult of Diablos and he wants to use Shadow Garden to stop them.
But one day he’s hit by a truck and dies, causing him to be reborn in a fantasy world (which is when he takes on the name of Cid Kagenou).
Funny enough, the made-up stories that he believed at first areactually truein this fantasy world and he’s really fighting enemies.
Shadow Garden started as a small unit with only a few members, but they eventually expand their manpower, resources, and base of operations to be able to match the Cult of Diablos.
4. SWORD (One Piece)
SWORDis a secret branch of the Marines inOne Piece. On the surface, they operate very much like the regular Marines: they hunt pirates, they protect countries, they do all the usual things.
What sets them apart is that they aren’t directly under the jurisdiction of the Marines or the World Government, meaning they have the freedom to act of their own will and can perform whatever missions they want without needing permission from higher-ups.
That being said, the Marines and World Government take no responsibility for the actions of SWORD, and will even hunt them down or eliminate them if they cross the line and harm the name of the Marines or World Government.
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3. The Swordsmiths (Demon Slayer)
Swordsmithsfrom the Swordsmith Village play one of the most crucial roles for the Demon Slayer Corps. Why? Because they’re the ones who provide the Nichirin swords to the Demon Slayers, which are their primary weapons for killing demons.
And yet, even though they forge the swords, they aren’t swordsmen and they aren’t suited for battle, so their existence is kept a secret—even some Demon Slayers don’t know of them.
To further conceal the Swordsmith Village and its residents, they follow strict measures: any member of the Corps who visits the village needs blindfolds, earplugs, noseplugs, and must ride several Kakushi (a brigade of attendants) to get there.
The villagers also hide their own identities by wearing masks to keep themselves—and the village—safe and a total secret.
Related:The Coolest Anime Swords and the Stories Behind Them
2. WISE (Spy X Family)
InSpy X Family, the Westalian Intelligence Services' Eastern Division (orWISE) is an organization that exists to keep the peace between Ostania and Westalis, two nations on the brink of war.
They exist in absolute secrecy while working to prevent and eliminate threats that could disrupt the fragile peace they currently have. Twilight (who took on the assumed name Loid Forger) is the greatest spy currently working for WISE.
For his latest mission, he needs to create a fake family in order to infiltrate an elite school and get close to a political target. In doing so, he comes to know Yor Forger and Anya Forger, resulting in one of the best anime families we’ve seen.
Related:The Best Anime Clans and Families, Ranked
1. Akatsuki (Naruto Shippuden)
Originally,Akatsukiwas headed by Yahiko, with one established goal: to bring peace to the Hidden Rain Village.
Following Yahiko’s death and the involvement of Obito from the shadows, Akatsuki’s organizational structure underwent change and Nagato emerged as the new leader (complete with access to some of the more powerful abilities of the Rinnegan).
While peace remained Akatsuki’s primary goal, the way they sought to bring peace shifted. Assuming the identity of Madara Uchiha, Obito influenced Nagato to bring about the Infinite Tsukuyomi, which would trap the entire world under the illusion of peace.
To accomplish this, they would need to capture all the Jinchuriki in the world and extract their Tailed Beasts.
And so, this new Akatsuki recruited all kinds of powerful rogue ninjas from different nations, including Itachi Uchiha of the Leaf, Deidara of the Stone, Kisame of the Mist, and Sasori of the Sand.
With its array of interesting characters and iconic black-robe-red-clouds designs, Akatsuki cemented itself as one of the coolest secret organizations in anime—one that’s still memorable today.
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