While Percy knows he's the son of Poseidon, the Greek god of the sea, his mother Sally Jackson, has kept the truth of his father's identity a secret from him for years. She's done this to protect him from the dangers that come with being a demigod.
This secret is revealed in the book, and it becomes a major plot point as Percy and his friends search for the Golden Fleece to cure his friend, Grover Underwood, from the curse of the Fury Alecto.