Sometimes, the villainous organization doesn't go out and call itself The Empire or The Syndicate. Instead, they prefer to give themselves a feeling of unity in their nefarious and evil purposes. Calling yourselves "The Brotherhood" doesn't sound that evil, but nevertheless it seems to be a popular name among evildoers in fiction. Though the name indicates an organization of equals, there still tends to be one "big brother" in charge regardless.
The Brotherhood of Evil may function like The Mafia, or as a secret society with shadowy rituals and complex codes of honor, and are much less likely to invoke We Have Reserves on their "brothers" unless their sinister leader is just using them for their own purposes. If they're Card Carrying Villains, they might put a "Dark" or "Evil" in their name just to be clear that they're not the good kind of brotherhood.
- The Brotherhood of Evil Mutants, Magneto's supporters in the X-Men comics, which keeps the "evil" in its name despite often having sympathetic motives. They'll tell you they call themselves "evil" ironically— bigoted humans think we're the boogeyman? Let's be the boogeyman! The irony is lost on everyone else.
- The Brotherhood of Evil from Doom Patrol (which started out as a international crime syndicate, but we only ever saw their top people.)
- The Brotherhood of Metallix from Sonic the Comic.
- The Brotherhood of Dada in DC Comics, opponents of the Doom Patrol.
- Played with the Brothers in Perfect Creature, an Christian vampire order who teaches their members they are superior to mankind, but are also sworn to serve, educate and guild them as well. Sure enough, they are viewed considered heroic by most people... Except they are revealed to be extremely corrupt, hypocritical and responsible for the movie's crisis.
- In Thunderball, SPECTRE has "The International Brotherhood for the Assistance of Stateless Persons" as one of its covers.
- The Grail Brotherhood from the Otherland series.
- The dark elves of Midkemia are known as the Brotherhood of the Dark Path.
- Gender Flipped example: the Sisters of the Dark in The Sword of Truth
- The predecessor of the modern Sith Order was the Brotherhood of Darkness, elaborated on in the Star Wars Expanded Universe.
- The LLF Power Trio of Polly Star, La Chacala and Lady Dinamita are known as La Hermandad, a sisterhood of rudas.
- Call of Cthulhu. The Brotherhood of the Beast in the The Fungi from Yuggoth campaign (and its remake Day of the Beast).
- BIONICLE: The Brotherhood of Makuta under Teridax's rule, mostly because he killed most of the Makuta who actually still had functioning moral compasses, with the exception of Krika.
- Sonic Chronicles: The Dark Brotherhood
- The Brotherhood Of Nod from the Command & Conquer: Tiberian Series.
- The Elder Scrolls series has the Dark Brotherhood, an illegal assassin's guild who practices a Religion of Evil, serving Sithis, their "Dread Father", who is an Anti-God personification of the primordial force of chaos and is represented by a "great void".
- The Brotherhood of the Dark Rapture from Clive Barker's Jericho.
- The Brotherhood of the Ninth Circle, a doomsday cult led by an insane vampire, from Vampire: The Masquerade Bloodlines.
- Just about any organizations in video games that even involve the word 'brotherhood'.
- Although in Assassin's Creed, the (relatively) good Assassins call themselves "The Brotherhood", while the Templar Order decidedly fits this trope perfectly.
- Played with in the Fallout series with the Brotherhood of Steel. They're not evil, per se, but they've made many enemies due to their aggressive hoarding of pre-war technology, and have been known to murder people to preserve their secrecy. On the other hand, they have wiped out troublesome raider groups such as the Vipers, and have played a major role in the defeats of the Enclave and the Super Mutants.
- The Brotherhood is one of the rival gangs in Saints Row 2.
- The Assembly of Evil from LessThanThree Comics' Brat Pack, although, to be fair, they are supposed to be used as a propaganda tool for when their boss runs for President.
- The Sith Brotherhood and Brotherhood of the Sith in The Gungan Council.
- Darkwing Duck deters criminals from FOWL, the "Fiendish Organization of World Larceny."
- The Mafiya is also known as "Bratva", which means, you guessed it, "Brotherhood".