Maester Aemon was a wise and learned member of the Night’s Watch who served for many years as a mentor and advisor to Jon Snow. Although there is no explicit evidence in the books or the show to suggest that Maester Aemon knew about Jon’s true parentage as a Targaryen, there are several clues and hints that suggest that he may have suspected or even known the truth.
One of the most significant pieces of evidence comes from the conversation between Maester Aemon and Jon Snow in A Storm of Swords, when Jon is contemplating breaking his vows to the Night’s Watch and riding south to aid his family in the war of the Five Kings. Maester Aemon tells Jon about his own family, including his great-grandfather, King Daeron II Targaryen, and his uncle, King Aegon V Targaryen. Maester Aemon reflects on his own choices, saying, “Egg had an innocence to him, a sweetness we all loved. Kill the boy, Jon Snow. Winter is almost upon us. Kill the boy and let the man be born.”
Many readers and viewers have interpreted this as a reference to Jon Snow’s own situation, with “Egg” being a nickname for Aemon’s uncle, Aegon V Targaryen. Aegon V was known for his attempts to break the power of the great lords and promote social reform, but he also had a personal connection to the Night’s Watch, having served there himself as a young man. By encouraging Jon to “kill the boy,” Maester Aemon may have been urging him to let go of his ties to his family and embrace his duty to the Night’s Watch, just as Aegon V had done before him. However, it’s also possible that Maester Aemon was hinting at Jon’s own Targaryen heritage, and suggesting that he needed to embrace his true identity and become the man he was meant to be.
Another piece of evidence comes from the way that Maester Aemon refers to Jon Snow throughout the books and the show. Despite his position as a maester and a member of the Night’s Watch, Aemon is still a Targaryen at heart, and he often uses the Targaryen family motto, “Fire and Blood,” to describe Jon. In A Storm of Swords, for example, he says, “Love is the death of duty. If the day should ever come when your lord father asks you to betray the Night’s Watch, send me your head and I’ll return it to him…burning.” This use of the word “burning” suggests a connection to the Targaryen tradition of using fire to dispose of their enemies, and it may be a subtle clue that Aemon is aware of Jon’s true identity.
Furthermore, there are hints that Aemon may have been aware of the secret Targaryen history that is revealed in A Dance with Dragons. In that book, we learn that Rhaegar Targaryen secretly married Lyanna Stark and that Jon Snow is their son. This information is revealed through the memories of several characters, including Bran Stark, who sees the wedding in a vision, and Daenerys Targaryen, who hears about it from the loyalists who remained with her family after Robert’s Rebellion. While there is no explicit evidence that Maester Aemon knew about this secret marriage, he was one of the few people left in Westeros who would have had the knowledge and expertise to recognize the significance of the prophecy of the Prince That Was Promised, which is strongly connected to the Targaryen bloodline.