Warning: Spoilers for House of the Dragon Season 1
As we know, bloodlines in Westeros can be hard to keep track of. When it comes to the Targaryens, it’s difficult mostly because their names are all very similar if not the same, and that may be because their bloodline has kept its strong Valyrian roots, meaning, there was a lot of inbreeding amongst the members of the House of the Dragon.
But Rhaenyra’s children, Jacaerys, Lucerys, and Joffrey, are only half Targaryen, an unusual occurrence for the time. Their brown hair is a tell-tale sign that they are not pure descendants from Old Valyria, lacking the silver locks that distinguish both Targaryen and Velaryon.
That is one of the issues that certainly contributed to the civil war we see erupt by the end of Season 1: the rumored illegitimacy of Rhaenyra’s children, who were supposed to be her husband’s, Laenor. But the two, even though they tried, as Rhaenyra told Daemon, never managed to conceive.
So, who’s the father?
The father was Harwin Strong. Rhaenyra can be seen dancing with Harwin during the ball in episode 5, but it is not until episode 6 that we see that something more bloomed between them during the years of timeskip. In this episode, the two can be seen exchanging glances that are pretty telling of the nature of their relationship. Furthermore, other characters including Alicent and Ser Criston, are also implicitly vocal in their awareness of what transpired between Rhaenyra and Harwin.
Some people, even after all the clues, were left unsure about whether Ser Criston Cole could have also been the father. However, that is highly unlikely. Everything points to Harwin – not Criston, who’s decidedly bitter about Rhaenyra’s choices – being the father. The timeline would not have made sense, as Rhaenyra and Criston seem to have broken off their romance way before Rhaenyra ever became pregnant. Harwin also behaves like a doting father towards Rhaenyra’s children – as much as he deems it safe – when they are sparring against Alicent’s sons, whereas Cole is ruthless and harsh, seemingly as a means to get back at the Princess.
As for Rhaenyra’s other two sons, the twins, Aegon and Viserys, they are Daemon’s children. Not that anyone, viewers or characters, have any doubts about that.