For the majority of HBO’s hit show Game of Thrones, we’re led to believe that Jon Snow is the bastard son of Ned Stark. Toward the end of the show’s run we find out that’s not the case. So who are his parents?
The show’s final episode confirmed a fan theory that Ned was not his father at all, but that he raised Jon as his own due to some unfortunate circumstances. The truth is that Jon’s parents are Lyanna Stark and Rhaegar Targaryen, something that only a few people in the Seven Kingdoms know about.
Lyanna Stark is Ned’s sister and Rhaegar Targaryen is the son of Aerys II Targaryen, also known by the moniker “The Mad King.” This means he’s also Daenerys’ older brother. Lyanna was Rickard Stark’s only daughter.
Both were married before they decided to run off together and set off a chain of events that would lead to countless deaths and political troubles. Rhaegar was married to Elia Martell and Lyanna married Robert Baratheon. They decided to leave their spouses and run off and get married in a secret ceremony – the same ceremony we witnessed through Bran’s vision.
This brings up another question. Why did Ned hide Jon’s real parentage in the first place? Well, when the two lovebirds ran off together, it created a rift in the Kingdoms and became the catalyst for Robert’s rebellion which overthrew the Targaryen Dynasty.
Instead of believing the truth, most people instead stuck to the story that Rhaegar kidnapped his new wife. This made her brother Brandon and her father to look for retribution. Things quickly got out of control and spiraled into a huge war.
Robert murdered Rhaegar during battle and Jaime Lannister killed the Mad King, which put Robert on the throne. Newly crowned but looking to consolidate his power, he desperately wanted Daenerys dead (as seen in season one). If he knew Jon’s true lineage, he would have killed him as well.
Ned, for his part, honored his sister’s dying wish and raised Jon as his own bastard child. He told everyone he fathered Jon during the war and he kept his word and never told anyone the truth, including his wife Catelyn. This is the reason she hated Jon so much.
Because Rhaegar was the heir to the Iron Throne and he was killed, Jon is the next person in line. He also had a stronger claim than Daenerys, his aunt, because he’s an actual heir and not a lateral relative.