The 18-times Olympic gold medallist led all the way in an event he has owned during most of his decorated career, clocking 1:59.39 to win by more than a second at the outdoor pool in Santa Clara.
The time ranks the American 18th in the world this year in an event he has won three times at the Olympics.
It was also more than three seconds slower than he swam to finish second at last year’s Pan Pacific Championships in Australia.
Phelps did not peak for the Santa Clara meet. He is aiming for the national championships in San Antonio in August and, more importantly, next year’s Rio Olympics.