Kitajima became the first person to win the event in two straight Olympics and did so in the world record time of 58.91.
Alexander Dale Oen of Norway took the silver, becoming the first person from his country to win an Olympic swimming medal. The bronze went to Hugues Duboscq of France.
American Brendan Hansen, who owned the world record Kitajima broke, finished fourth. Hansen was runner-up to Kitajima four years ago in Athens.
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