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. This is averted in most adaptations, where the name is generally streamlined to just "The Brotherhood of Mutants." Even in the comics they very rarely call themselves the Brotherhood of Evil Mutants anymore, due to comics shifting away from obvious Card Carrying Evil type villains.
- The Brotherhood of Evil from Doom Patrol (which started out as an international crime syndicate, but we only ever saw their top people). They also showed up as Big Bads of the final season of Teen Titans.
- Red Robin: The Daughters of Acheron are a group of unrelated villains who usually work alone but will come to the aid of their "sisters" when asked and are willing to die for each other's plots. One of them is the biological sister of Ra's Al-Ghul and the Demon's Head is able to turn her attention to Tim.
- Wanted: The Fraternity, a group uniting the world's supervillains. After killing all the superheroes, they divided up the world between their ruling Council Of Five, with each members getting control over organized crime on a continent. They're now so powerful they've gained complete impunity, with displaying Fraternity pins or license plates being enough to get away with any crime (including killing cops. However, they still hide from the general public for their own convenience.
- Played with by the Brothers in Perfect Creature, a Christian vampire order which teaches their members they are superior to mankind, but are also sworn to serve, educate and guild them as well. Sure enough, they are considered heroic by the population... Except they are revealed to be extremely corrupt, hypocritical and responsible for the movie's crisis.
- A gender flipped example: the Sisters of the Dark in The Sword of Truth, an organization of evil sorcerers within the Sisters of the Light secretly serving the Keeper.
- The predecessor of the modern Sith Order was the Brotherhood of Darkness, elaborated on in the old Star Wars Legends books. Founded by a Jedi Master turned Sith Lord, they essentially mimicked the Jedi Order, arising from the ashes of the Sith Empire in the Republic's Dark Age. They waged war on the Jedi and Republic until both side's armies slaughtered each other at Rusaan. Their infighting weakened them, so that sole survivor Darth Bane decided to institute the Rule of Two in the Sith Order he founded afterward, with only a master and apprentice operating from the shadows against the Republic/Jedi instead of openly fighting them. The new Expanded Universe has indicated they were the same, though with less detail.
- 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.
- 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 Ninth Circle, a doomsday cult led by an insane vampire, from Vampire: The Masquerade Bloodlines.
- 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, a bunch of monster truck-driving tattooed metalheads, is one of the rival gangs in Saints Row 2.
- League of Legends (and to a larger extent, its spinoff Legends of Runeterra) features a faction known as the Navori Brotherhood, an aggressive ultra-nationalist group from the island nation of Ionia. It was originally formed to protect Ionia as it was being invaded by Noxus, but following Ionia's victory, the brotherhood sought to reunite the now-splintered Ionia under their control, becoming akin to domestic terrorists to those unwilling to submit. Their biggest atrocity was enlisting Jhin — a long-imprisoned Mad Artist and Serial Killer — to commit mass-killings across Ionia and blame them on foreigners in an attempt to unite Ionia through fear and jingoistic revenge.
- The Mafiya is also known as "Bratva", which means, you guessed it, "Brotherhood".