Rhaenyra's longest-lasting relationship is with her uncle, Prince Daemon Targaryen. In addition to the age gap and the incest, their relationship starts off on an especially controversial foot, with rumours that he either seduced her or taught her to seduce Ser Criston Cole, resulting in his exile. In the book, Daemon was married twice before, first to Rhea Royce, then to Laena Velaryon, sister of Rhaenyra's husband, Laenor.
However, both Velaryon siblings die, leaving Rhaenyra and Daemon both widowed and with children. Months later, Rhaenyra and Daemon marry, causing scandal with the sudden nature of their marriage and with its secrecy, performed without King Viserys's knowledge or permission. Nevertheless, their marriage is ultimately accepted, and they have two sons, Aegon and Viserys.
Daemon and Rhaenyra's relationship lasts through the Dance of the Dragons, with Daemon as Rhaenyra's staunch supporter. Ultimately, neither survives the war, but their sons both become kings in time, and their descendants continue the Targaryen royal line until the end of the royal house centuries later.