Phelps, 22, was clocked in 4:05.25, breaking his own world record of 4:06.22.
Ryan Lochte also broke the old record, placing second in 4:06.08,
The top two finishers in each event qualify for the Games.
Phelps won eight medals at the 2004 Olympics in Australia -- six gold and two bronze.
The young star is entered in eight events at the trials.
American Mark Spitz holds the record for the most gold medals at a single Olympics, having won seven in Munich 32 years ago.