On Day 2 of the 2021 MLB Draft, the Marlins selected the following players:
- Round 2, No. 52 overall pick—Cody Morissette, SS, Boston College (ranked 46th overall on Baseball America/59th on MLB Pipeline/72nd on Prospects Live)
- Round 3, No. 88 overall pick—Jordan McCants, SS, Pensacola Catholic HS (FL) (ranked 89th/133rd/152nd)
- Round 4, No. 118 overall pick—Tanner Allen, OF, Mississippi State (ranked 168th/136th/119th)
- Round 5, No. 149 overall pick—Brady Allen, OF, South Carolina (ranked 178th/193rd/331st)
- Round 6, No. 179 overall pick—Sam Praytor, C, Alabama (ranked UR/UR/447th)
- Round 7, No.