It was Phelps's third victory in the Beijing Games and the ninth of his Olympic career. That ties him with runner Paavo Nurmi, gymnast Larisa Latynina, swimmer Mark Spitz and track star Carl Lewis for the most Olympic gold medals.
Phelps remains on track to break Spitz's record of seven gold medals in a single Olympics.
The silver medal Tuesday went to Tae Hwan Park of South Korea and the bronze to American Peter Vanderkaay.
Phelps's time of 1:42.96 broke his own world record of 1:43.86.