The Farseer Trilogy by Robin Hobb
From Assassin's Apprentice:
Young Fitz is the bastard son of the noble Prince Chivalry, raised in the shadow of the royal court by his father’s gruff stableman. He is treated like an outcast by all the royalty except the devious King Shrewd, who has him sectetly tutored in the arts of the assassin. For in Fitz’s blood runs the magic Skill–and the darker knowledge of a child raised with the stable hounds and rejected by his family. As barbarous raiders ravage the coasts, Fitz is growing to manhood. Soon he will face his first dangerous, soul-shattering mission. And though some regard him as a threat to the throne, he may just be the key to the survival of the kingdom.
From Royal Assassin:
Young Fitz, the illegitimate son of the noble Prince Chivalry, is ignored by all royalty except the devious King Shrewd, who has had him tutored him in the dark arts of the assassin. He has barely survived his first, soul-shattering mission, and returns to the court where he is thrown headfirst into the tumult of royal life. With the King near death, and Fitz’s only ally off on a seemingly hopeless quest, the throne itself is threatened. Meanwhile, the treacherous Red Ship Raiders have renewed their attacks on the Six Duchies, slaughtering the inhabitants of entire seaside towns. In this time of great peril, it soon becomes clear that the fate of the kingdom may rest in Fitz’s hands–and his role in its salvation may require the ultimate sacrifice.
From Assassin's Quest
From an extraordinary new voice in fantasy comes the stunning conclusion to the Farseer trilogy, as FitzChivalry confronts his destiny as the catalyst who holds the fate of the kingdom of the Six Duchies…and the world itself.
King Shrewd is dead at the hands of his son Regal. As is Fitz–or so his enemies and friends believe. But with the help of his allies and his beast magic, he emerges from the grave, deeply scarred in body and soul. The kingdom also teeters toward ruin: Regal has plundered and abandoned the capital, while the rightful heir, Prince Verity, is lost to his mad quest–perhaps to death. Only Verity’s return–or the heir his princess carries–can save the Six Duchies.
But Fitz will not wait. Driven by loss and bitter memories, he undertakes a quest: to kill Regal. The journey casts him into deep waters, as he discovers wild currents of magic within him–currents that will either drown him or make him something more than he was… ~Robin Hobb's website