In the real world, the issue with inbreeding is that it increases the risk of a recessive genetic disorder popping up. In fiction, it seems that one of the most common recessive genetic disorders is evil.
The reasons for this are varied. Taboos against incest are strong and have only gotten stronger with time and just as illegitimate children and children of rape have historically been shamed for their irregular parentage, so too are children of incest. This shaming may be strengthened by the fact that, outside of certain royal families or cases of Surprise Incest, children of inbreeding are likely to be illegitimate and/or the products of rape, worsening the negative connotations associated with them.
Alternately, inbreeding may provide a convenient and less ableist justification for the employment of certain tropes. Need to explain how the isolated Cannibal Clan keeps recruiting, and why its members are deformed, disabled, or mentally handicapped? Want a reason for why The Caligula is so Royally Screwed Up? Blame a recessive genetic disorder or hereditary mental illness and claim that the issues were exaggerated by generations of inbreeding.
Finally, incest and inbreeding may serve as a Freudian Excuse of sorts for a villainous character. The kind of person who would deliberately engage in incest is not, after all likely to be breathtaking parental material and their treatment of the children who result from their activities is liable to be atrocious. Said children are also likely to learn some very warped lessons about appropriate social behaviour and sexual mores from such a parent; more than one Serial Rapist has had incestuous parentage in the backstory.
A staple of the Hillbilly Horrors genre, this trope can be nevertheless be found on both ends of the villainous socioeconomic spectrum, overlapping with Aristocrats Are Evil as often as it does with rural Bandit Clans and Cannibal Clans. Often overlaps with Bastard Bastard and Child by Rape. See Red Right Hand, Evil Cripple, Mental Handicap, Moral Deficiency, and The Caligula for what the trope might be used to explain away.
- One memorable villain from The Authority was Seth Angus Billy Cletus Bubba Jamie Clement Cowie, a hillbilly given Combo Platter Powers by world governments specifically to take down the Authority (and nearly succeeded, receiving a harem of children as a reward). His birth came about around nine months after his mother was stuck in a cabin with her seven brothers, and after his defeat was transformed into seven chickens and returned to his uncles.
- Hot Fuzz has Lurch, a mentally deficient thug who serves as the villain's muscle and whose grandfather was also his father.
- While this was absent from the original Texas Chainsaw Massacre and its sequel, later installments in the franchise declared that Leatherface's oldest brother was also his father, and that most of cannibalistic Sawyer clan were products of Villainous Incest.
- Wrong Turn features The Mountain Men, a clan of inbred cannibal hillbillies who have become mutant freaks courtesy of isolation and inbreeding.
- The 1973 movie Death Line (US title: Raw Meat) features a cannibal clan hiding in the London subway system, the result of an 19th-century dig accident trapping a bunch of male and female workers in the tunnel system. By the time of the events in the film, there are only two exceedingly sickly, barely-human descendants remaining.
- Excalibur makes Mordred the son of Arthur and his half-sister Morgana (rather than his half-sister Morgause) and even more insane than he usually is. In the end he not only destroys Camelot, but murders his mother in a fit of rage before going down to a Mutual Kill with his father.
Mordred: "Come father, let us embrace at last!"
- A Song of Ice and Fire:
- Jaime and Cersei Lannister have a long-term twincestuous relationship going on, and they have three kids together. We know dwarfism is a genetic disorder that's present in their family—their brother Tyrion is a dwarf—but all three of their kids are of normal height. The eldest, Joffrey, is a blatant case of The Caligula however, and it's heavily implied that this is the product of not one, but two generations of inbreeding (Cersei and Jaime's father married his cousin) coming back to bite them
- In-universe, the Targaryen habit of marrying their sisters is often viewed as having exacerbated the hereditary madness that crops up again and again in the family, producing a series of warped aristocrats including Maegor the Cruel, Aerion Brightflame, Aerys the Mad, and Viserys the Beggar King within the main family line, and equally, if not even more depraved characters like Daemon Blackfyre and Maelys the Monstrous in the bastard Blackfyre branch of the family.
- In Harry Potter and the Half-Blood Prince, Dumbledore says he partially attributes the mania of the Gaunt family to frequent marriage between cousins in an effort to keep the bloodline pure.
- Dean Koontz:
- Whispers: "Bruno Frye" is the collective name for a pair of murderous twins whose father was also their grandfather. Left completely unbalanced by her father's assault on her, Katharine Frye raised her twin boys to think of themselves as one person, and to see sexuality as a product of the Devil. The two become Serial Killers who hunt down and murder women they believe to be possessed by the Devil.
- The Bad Place: Candy Pollard's grandfather was an incestuous rapist who impregnated his mentally handicapped younger sister. His mother was the hermaphroditic child of that union, who went onto repeatedly impregnate herself, producing four children, all with Psychic Powers. While youngest son Frank is emotionally damaged but moral, and twins Violent and Verbina are feral and amoral but not necessarily malicious, Candy is a genetically damaged, physically deformed monster, born with two sets of testicles and no external genetalia, who uses his teleporting and telekinetic abilities to become a serial murderer of the women he desperately wants to, but physically cannot have, sex with.
- H.P. Lovecraft did this a few times.
- In "The Lurking Fear" the monsters terrorizing a small town turn out to be the inbred descendants of a once prominent family, who retreated underground and began marrying their own once their reputation got too ugly.
- In "The Dunwich Horror" it's heavily implied that when Yog-Sothoth fathered Wilbur and his brother on Lavinia Whateley, he did so while possessing her father Old Wizard Whateley.
- Murder in Advent by David Williams has the Daras family, who were aristocrats a few centuries back, and are now reduced to an evil old recluse and his harem of female relatives, holed up in what was their estate's home farm.
- Robert Louis Stevenson's short story "Olalla" plays with this. When the soldier protagonist is sent to recuperate with a decayed noble family in Spain, he discovers that the family's isolation has resulted in extensive inbreeding, leaving them all with the same set of recessive traits, most notably flaming red hair, in addition to leaving the son, Felipe, and the unnamed mother, intellectually disabled. The protagonist nevertheless falls in love with the family's beautiful daughter, Olalla, and is pursuing a romance with her when he receives a cut on his hand that prompts the mother to attack him and try to eat him. Olalla sends him away after that, informing him that her family is too damaged for him to become a part of.
- The Jack Ketchum novels Off Season and Offspring have an inbred cannibal family stalking and killing people that they think are trespassing on "their territory".
- Phil Rickman's The Wine of Angels features a reclusive farming family whose sons are expected to lose their virginity to their mother before going out to rape and murder innocent victims.
- Criminal Minds: The Killer Woodsman from Season 9's "Blood Relation" is the result of an incestuous relationship between siblings Malachi and Magdalene Lee, who abandon him due to his deformities. Years later he begins stalking his parents and their new families, killing off his half-siblings in a rage at having been considered worthless.
- Game of Thrones:
- As in the novels, Jaime and Cersei Lannister are in an incestuous relationship, and as in the novels their oldest son Joffrey is The Caligula, this time with a side of sexual sadism atop his random acts of cruelty, murder, and domestic violence.
- Also as in the novels, the Targaryen family has a proud history of marrying cousin to cousin, uncle to niece, and brother to sister, producing the likes of Aerys the Mad and his equally unhinged son Viserys the Beggar King.
- Law & Order: SVU has Darius Parker, whose father was also his grandfather. Emotionally abused by his mother, who was never able to forget how he was conceived Darius grew up to be a murderer and a rapist himself.
- Theodore "T-Bag" Bagwell from Prison Break and Breakout Kings is a Serial Killer and Serial Rapist who is revealed to be the product of incestuous rape between his father and his father's mentally handicapped sister. It's made pretty clear that T-Bag never really had a chance of being anything other than a villain, with Lloyd noting that "some machines just come off the assembly line broken." T-Bag himself revealed at one point that he was sterile, so the family line would end with him.
- On Supernatural, there have been two different episodes in which the villain ends up being an inbred human.:
- In the episode The Benders, a clan of hill folk are kidnapping people and hunting them for sport. It is heavily implied that that the younger members are products of incest and likely also engaging in incest with the only female member of the clan.
- In the episode, Family Remains, a suspected series of ghost murders turns out to have been committed by feral twins born out of the incestuous rape of their mother/sister by their father/grandfather, which led to the mother/sister killing herself out of shame and the twins killing the father/grandfather out of rage. They then hid in the walls of the home to avoid detection but emerged to kill anyone who tried to inhabit the house.
- The X-Files featured an episode, to great controversy, about a murderous, inbred clan known as the Peacock family . The matriarch, Mrs. Peacock, is involved in incestuous relationships with her sons, one of them being the father of the other two.
- Hunter: The Vigil: Inbreeding is offered as an explanation for the deformities of both the Freak and Mutant Slasher Undertakings, with the disfigurements either arising from genetic disorders or from the inbreeding reinforcing a supernatural taint in the family.
- Ogres are modeled on the Hillbilly Horrors and Cannibal Clan stereotypes, and as such, are not only willing to inbreed, but actively prefer it, marrying as close to the family line as possible, with parent-on-child, sibling-on-sibling and other combinations being a feature of Ogre life and resulting in ever more deformed offspring. Their half-human relatives, the degenerate Ogrekin are just as prone to inbreeding, and entire forests are haunted by families of Ogrekin with minds as twisted as their family trees.
- The Ogre penchant for inbreeding is inherited from their parent race, the Hill Giants, who while not as fond of it as the Ogres, are still willing to breed within the family, producing some young in the process who look only barely like the standard Hill Giant. Marsh Giants, descended from Hill Giants who fled into the swamps and were reduced to reproducing with boggards, demons, and their own kin, are if anything, even more warped than the Ogres and Ogrekin, with bloodlines sullied by incest, interspecies rape, and demonic taints.
- Warhammer: Sigvald the Magnificent, the Champion of Slaanesh, was born of a particularly depraved chieftain who ended up bedding his own sister. Sigvald continued in his father's footsteps until he tried to overthrow him, his excesses bringing him to the attention of Slaanesh, and now merrily rapes, tortures and burns his way through the world at the head of his army.
- Fire Emblem: Genealogy of the Holy War: Julius was born of an incestuous relationship and bears the lineage of the evil dragon Loptyr.
- Sayo from Umineko: When They Cry is the product of her grandfather raping his illegitimate daughter due to believing that she was her mother's reincarnation. As a result, Sayo was hidden away, which is one of the reasons she's so messed up. While most likely not outright evil, Sayo is the Greater-Scope Villain of the series.
- In Ben 10: Alien Force, the Highbreed, an alien species so obsessed with genetic purity that they seek to exterminate all other races due to their "inferior" gene pool, are stated to all be inbred and sterile.