InGame of Thronesseason 1, episode 7 “You Win or You Die,” Lord Eddard Stark confronts Cersei Lannister about the nature of her and her twin brother, Jaime Lannister’s relationship. Without feeling an ounce of shame, Cersei says the Targaryens wed brothers and sisters for three hundred years to keep bloodlines pure, thereby prodding Ned to regard her and Jamie’s relationship in the same light.
Cersei is partially right, as the prequel toGame of Thrones-House of the Dragon(2022) featured Viserys I Targaryen’s second wife, Alicent Hightower betroth her son, Aegon to daughter, Helaena in the tradition of House Targaryen. Therefore, the question remains of why Cersei and Jaime’s relationship was considered illicit inGame of Throneswhen Aegon II fromHouse of the Dragonhad simply performed his duty in marrying Helaena.

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The answer lies in House Targaryen’s long-standing practice of marrying brothers to sisters to perpetuate its Valyrian lineage. It’s a well-known fact that the erstwhile ruling Targaryen dynasty of Westeros was the Blood of Old Valyria, in that, their ancestors were the natives of theValyrian Freehold (before a volcanic cataclysm destroyed it)and one of the great dragonlord families. The Valyrians were no strangers to these types of marriages and married brother to sister, uncle to niece, and aunt to nephew to preserve their features. This explains why Aegon the Conqueror married his elder sister, Visenya out of duty to secure his succession. He also took his younger sister, Rhaenys as his second wife purely out of love. Aegon’s sister-wives aided him in the conquest of Westeros, and they bore him two sons; Aenys I from Rhaenys and Maegor I from Visenya.
The Faith Militant Uprising
While Aegon handled the Faith’s reservations with skill and sensitivity, his son, Aenys who inherited the Iron Throne after him, was rather tactless.Aegon the Conquerorwas cordial with the Faith of the Seven, and the opinions of the High Septons were compelled to silence because House Targaryen had conquered most of Westeros, and possessed dragons. The Faith turned a blind eye to the situation, in that, they neither denounced nor upheld Aegon’s marriages. That said, there existed humbler members of the Faith who held firm beliefs and considered Aegon’s marriages violative of the Faith’s rules.
Aegon and Rhaenys' son, Aenys I was married to his cousin Alyssa Velaryon, and she bore him six children, the eldest being a daughter, Rhaena. While Visenya suggested that her son, Maegor be married to Rhaena to secure the succession, the High Septon, Aenys, and Alyssa objected to the match. Maegor’s first wife was the High Septon’s niece, Lady Ceryse Hightower, and because she bore him no children, he took a second wife - Lady Alys Harroway. Maegor and Alys' marriage set tongues wagging inthe Seven Kingdomsand many objected to it. After failing to convince the Septon at Dragonstone to officiate the wedding, Maegor wed Alys in a Valyrian wedding ceremony, led by his mother, the Dowager Queen, Visenya. While Aenys argued against the marriage, Ceryse Hightower’s brother, Ser Martyn demanded Maegor set his second wife aside and the High Septon deemed the marriage to be sinful. Maegor remained defiant claiming that the rules of the Faith did not apply to the blood of the dragon. He took an exile of five years, and Aenys meanwhile faced the militant uprising of the Faith.

King Jaehaerys' Doctrine of Exceptionalism
The military order of the Faith rose en masseagainst House Targaryenafter Aenys wed his son to his daughter. The Faith Militants killed Septon Murmison who had officiated the ceremony of Prince Aegon and Princess Rhaena and persecuted the lords who supported the king. The High Septon denounced the Targaryens, and this conflict lasted until the fourth Targaryen king, Jaehaerys I the Wise sat the throne. Aenys was overpowered in the uprising, he fled King’s Landing and took refuge at Dragonstone where he passed away. His half-brother, Maegor usurped the throne of his children and challenged the Faith Militants to a Trial of Seven, which the latter accepted. Lore says that only Maegor survived this trial, proving the throne was his to claim. He mounted Balerion promptly and burned down the Sept of Remembrance and hundreds of Faith Militants that prayed inside. Maegor’s war on the Faith became an intractable conflict and the truth is, no one knew how to respond to the concerns and reservations of the Faith until there came Jaehaerys the Wise.
Aenys’s son, King Jaehaerys I was a diplomat, like his grandfather, the Conqueror.House of the Dragonsays he reigned over nearly sixty years of peace and prosperity. This achievement is attributed to his desire to restore peace in the realm. He sought the reconciliation of the crown and the Faith and thanks to him, House Targaryen was accorded certain explicit rights. Jaehaerys and the High Septon agreed that as long as Targaryens defended the Faith, the Faith Militant would cease to exist. Targaryens were privileged to carry on this tradition. Moreover, it was agreed that the remaining members of the Faith Militant would be pardoned if they laid down their weapons. Jaehaerys' accord with the Faith Militant was generous considering how the armed rebellion had weakened by then.
Both sides stayed true to their word - the Faith Militant remained defunct for the next three centuries while the crown acted as the defender and upholder of the Faith. Thus, the Wise King’s descendants, Rhaenyra and Daemon were able to marry each other in a Valyrian ceremony inHouse of the Dragon. Besides being a sin in the eyes of the Faith and an illicit practice in the Seven Kingdoms, the negative effects, most notably genetic illnesses, persisted among members of House Targaryen. Due to frequent inbreeding, the Targaryens were infamous for being mentally unstable. The so-called ‘Targaryen madness,’ is exemplified by the well-known saying, “Every time a Targaryen is born, the Gods flip a coin.” In other words, the chances of Targaryens eventually succumbing to madness were high, as seen in the case ofDaenerys Targaryen inGame of Thrones.
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