Wilson was selected in the first round of the 1992 draft by the New York Mets. A center fielder, Wilson is the stepson of former major leaguer Mookie Wilson.
His major league debut was in 1998, and he was hitting .300 in his first eight games when he was traded along with Geoff Goetz and Ed Yarnall to the Florida Marlins for recently acquired catcher Mike Piazza. He would spend most of the season in the Marlins' minor league system, making an appearance for the club in September, going 2-for-31.
Wilson made the opening day roster out of spring training in 1999, his official rookie season. He would finish second in the voting for NL Rookie of the Year by compiling a .280 average along with 26 home runs and 71 RBIs.
In 2000, Wilson joined the 30/30 club by banging out 31 home runs and swiping 36 bases. He also had 121 RBIs and led the Majors with 187 strikeouts.
In four and a half seasons with the Marlins, Wilson hit .262 with 104 home runs and 329 RBIs and 87 stolen bases.
He was traded with Vic Darensbourg, Charles Johnson and Pablo Ozuna to the Colorado Rockies for Mike Hampton, Juan Pierre and cash.