Jon Snow's father is Rhaegar Targaryen, the late Prince of Dragonstone. Jon is actually the son of Rhaegar Targaryen and Lyanna Stark, who were secretly married before Jon's birth. This was confirmed in the TV series Game of Thrones through Bran Stark's visions and documents found by Samwell Tarly, which revealed that Rhaegar annulled his previous marriage and married Lyanna in secret. Jon was raised as the illegitimate son of Ned Stark to protect him from Robert Baratheon, who would have killed him had he known the truth