In Assassin's Creed III, Haytham Kenway's father is revealed to be Edward Kenway.
Edward is the playable protagonist of Assassin's Creed IV: Black Flag and an eighteenth-century Welsh privateer who becomes involved with the Assassin Brotherhood. His story takes place several decades before the events of Assassin's Creed III.
Haytham inherits the Kenway name but follows the Templar cause, creating a family conflict that drives much of Assassin's Creed III. The game initially presents Haytham as its playable opening character before shifting to his son, Ratonhnhaké:ton, commonly called Connor.
Edward is not Connor's father; he is Connor's grandfather. Connor's father is Haytham, while Edward's own fatherhood connects two major historical periods in the series.