With Jon and Daenerys expected to meet soon on Game of Thrones, some viewers are wondering exactly how they are related. Read on for more details. This post has spoilers through the Season 6 finale.
We learned in the Season 6 finale, “Winds of Winter,” who Jon Snow’s parents are, thanks to the Tower of Joy flashback that Bran Stark had. We learned that Jon Snow is not, in fact, Ned Stark’s son, but rather the child of Lyanna Stark (Ned’s sister).
Lyanna Stark gave birth to a baby boy while in the Tower of Joy, under Rhaegar Targaryen’s protection. For the longest time, the “official” story was that Rhaegar had kidnapped Lyanna because he was obsessed with her and raped her. But others believed that Lyanna was in love with Rhaegar and left willingly.
Rhaegar took Lyanna to the Tower of Joy, where she gave birth to Jon. After Ned found her dying in the Tower, she gave Jon to Ned and he swore to protect his nephew. She told him that Rob would kill the baby if he knew. This could only mean that Jon was not Rob’s son, but Rhaegar’s. (Another hint is that the King’s Guard was protecting Lyanna and her baby, and the guards only protect royalty.)
By the time Game of Thrones begins, Rhaegar is long dead. He was Daenerys’ and Viserys’ older brother, the oldest son of the Mad King Aerys.
That makes Jon part Targaryen and part Stark. Jon has a claim to the Iron Throne, as a direct grandson of the Mad King Aerys. (He only has a true claim if Lyanna secretly married Rhaegar. Otherwise, he’s a bastard child of Rhaegar.)
This also means that Daenerys is Jon Snow’s aunt.
Fans are hoping that Daenerys and Jon Snow will have some kind of romantic connection. As weird as the aunt-nephew thing is, it likely would be a plus in Dany’s book, since Targaryens tend to prefer marrying other Targaryens so they can preserve the bloodline. (Obviously this changed when Dany was married to Drogo, but that was for a completely different reason.)