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The 14-time Olympic gold medal winner also captured the 100 butterfly at the University of Minnesota pool.
Phelps pulled away from a strong field to win the 200, finishing in one minute, 46.88 seconds. He won the 100 butterfly in 52.26.
The 26-year-old American is the world record-holder in the 100 butterfly.
Phelps' anticipated showdown with fellow American Ryan Lochte in the two events fizzled when Lochte placed third in the consolation final of the 200 freestyle and eighth in the championship heat of the 100 butterfly.
The 200 freestyle included Phelps, Lochte, French teen phenom Yannick Agnel, Chinese world champion Zhang Lin and Ous Mellouli.
Agnel placed second in 1:48.10 while Mellouli, an Olympic gold medallist in the 1,500 freestyle, was third in 1:48.26.
On the women's side, Allison Schmitt captured the women's 200 freestyle in 1:55.82, ahead of 16-year-old Missy Franklin (1:57.13).
Franklin won the overall Grand Prix series title last year and is seeking her first Olympic berth.
Jessica Hardy defeated Rebecca Soni to win the women's 100 breaststroke final. Hardy finished in 1:06.42, with Soni placing second in 1:07.04.
Brendan Hansen, who is racing again after two years off, won the 100 breaststroke with a time of 1:01.13. The 30-year-old Hansen is a four-time Olympic medallist.
The Minnesota Grand Prix is the first of seven stops this season on USA Swimming's Grand Prix series.
