Jon Snow was a fan-favourite character during the days of Game of Thrones. For a long time, it was said that his father was Ned Stark through a fling with “a lowborn” woman named “Wylla.” Then, however, the show changed it up to make Lyanna Stark, Ned’s sister, Jon’s mother, and Rhaegar Targaryen, his true father.
However, in the books, Ned is Jon’s father though the mystery of who the mother is is still up in the air.
Jon’s Father Is Not Ned Stark
According to Jon’s GoT Fandom page (linked above), his “stepmother” Catelyn hated him because he was “Ned’s mistake.” However, Ned treated Jon like one of his own children, as he should have. He never told him that Lyanna was his mother or that Ned was his uncle rather than his father.
The reason the “Ned Stark is not your father” storyline came up is because Bran, one of Jon’s “half-siblings”, had a vision where he learned the truth about his aunt giving birth to Jon, who was born as Aegon Targaryen and was Rhaegar’s last living child.
Rhaegar Targaryen
In Game of Thrones, Rhaegar annulled his marriage to Elia Martell so he could marry Lyanna. Rhaegar had two children with Elia. A daughter named Rhaenys and a son, Aegon, both names used within the Targaryen family. Both children were killed during the Sack of King’s Landing.
He married Lyanna in secret, and Jon was conceived at some point. Rhaegar was later killed by Robert Baratheon, who was Lyanna’s betrothed.
