on july 4, 2012, lee was traded to the miami marlins for minor leaguers matt dominguez and rob rasmussen. he played his first game as a marlin the next day against the milwaukee brewers, and went 2-for-4 with a run in a win. he hit his first home run as a marlin, a grand slam, on july 17 against the chicago cubs. in 81 games for the marlins, lee failed to produce as miami expected, hitting just .243 while homering just 4 times in 338 plate appearances.