Jacaerys, Rhaenyra's eldest son, and his two younger brothers have spent their short lives surrounded by whispers that their real father was Ser Harwin Strong.
So, who is the real father of Rhaenyra's children? In the show and in George R.R. Martin's Fire and Blood novel, it is heavily implied that Ser Harwin Strong, a knight and the captain of the City's Watch, is the true father of Jacaerys, Lucerys, and Joffrey.
Rhaenyra has had a tough couple weeks. First, she finds out that her half-brother Aegon II has usurped the throne and that she will have to fight for her claim as queen. Then, she gives birth to a stillborn child. And finally she loses her second eldest son Lucerys to a dragon battle.
Jacaerys Velaryon Is Rhaenyra's Firstborn Son and Heir
Firstborn son of Rhaenyra and her first husband Laenor Velaryon, Jacaerys was affectionately known to his family as Jace.
House of the Dragon on HBO has a lot of drama, but none more significant than the paternity issue surrounding Princess Rhaenyra Targaryen's three oldest sons: Jacaerys Velaryon, Lucerys Velaryon, and Joffrey Velaryon. These issues and more came to a head in the episode “The Lord of the Tides.”
Laenor and Rhaenyra had three sons together: Princes Jacaerys 'Jace', Lucerys 'Luke', and Joffrey 'Joff' Velaryon. It was rumored that those sons of Rhaenyra's were actually fathered by her lover, Harwin Strong, called "Breakbones".
Daemon and Rhaenyra share two children together: Aegon III and Viserys II.
Daemon and Rhaenyra really commit to the whole "keeping the bloodline pure" thing by having three — count 'em, three — children together. So in addition to Rhaenyra's three sons with her first baby daddy Harwin (RIP), she has one daughter and two sons by baby daddy two, Daemon.
Daemon and Rhaenyra had two sons together, Prince Aegon the Younger, born in 120 AC, and Prince Viserys, born in 122 AC. In 126 AC, Rhaenyra urged the ill Lord Corlys Velaryon to name as his heir her second son, Lucerys Velaryon.
The episode doesn't really beat around the bush when revealing that Harwin Strong (Ryan Corr) is the father of Rhaenyra's children. He's there soon after baby Joffrey is born so he can meet him, and later on in the episode Jacaerys (Leo Hart) even asks his mom if Harwin is his real dad.
With him, she found a love so deep it filled the void in her heart, not to mention her womb. In 196 AC, the year of their marriage, she painstakingly produced a set of twins, Aegon and Aella.
In the books, they have three: daughter Visenya, who does not survive infancy; and two sons, Aegon III and Viserys II, who will grow up to be next Kings of the Andals, the Rhoynar, and the First Men.
In a poetic end to the deadly war, Rhaenyra's son with Daemon became King Aegon III. He was also wed to his cousin, Aegon II's daughter Jaehaera.
King Aerys II Targaryen ("The Mad King")
Aerys II is a direct descendant of King Viserys I Targaryen through his daughter Rhaenyra.
Like Laenor Velaryon's sexuality, it was a “known secret” in the Red Keep that Harwin Strong was the father to Rhaenyra's three children: Jacaerys, Lucerys, and Joffrey.
Prosthetic designer confirms: the baby was deformed
“When the babe at last came forth, she proved indeed a monster: a stillborn girl, twisted and malformed, with a hole in her chest where her heart should have been and a stubby, scaled tail. The dead girl had been named Visenya.
As the two dragons struggled in the Battle Above the Gods Eye, Daemon plunged from Caraxes, wielding his sword Dark Sister and stabbing it into Aemond's remaining eye. Both dragons crashed into the Gods Eye, and Vhagar drowned with Aemond's body still chained to the saddle while Caraxes died on the shore.
The shock of the loss of her father, combined with the Greens' ruthless betrayal sends her into early labor. Without modern medicine, a baby born so early had very little chance of survival in the best of circumstances - and in these terrible conditions the baby, a girl named Visenya, is stillborn.
It isn't explicitly stated in the show, but because we learn after episode six that all three boys have dark brown hair — and despite Rhaenyra and Laenor's matching blond color — it has been strongly implied that they are actually the children of Ser Harwin Strong, the Lord Commander of the City Watch.
When finally did give birth to the baby, it is said that the child had a hole where her heart should have been, a tail, and scales for skin—a monster, as her mother had cursed her to be.
In Fire & Blood, the book House of the Dragon is based on, Daemon and Rhaenyra go on to have two boys: Aegon and Viserys. Yup, another Aegon and another Viserys. They also have a daughter, Visenya, but she is sadly a stillborn baby.
One of the first times we see Rhaenyra as truly angry throughout the entirety of Season 1 is during the traumatic miscarriage of her daughter Visenya.