The Miami Marlins farm system consists of seven Minor League Baseball affiliates across the United States and in the Dominican Republic. Four teams are owned by the major league club, while three—the Pensacola Blue Wahoos, Beloit Sky Carp, and Jupiter Hammerheads—are independently owned.
The Marlins have been affiliated with the Single-A Jupiter Hammerheads of the Florida State League since 2002, making it the longest-running active affiliation in the organization among teams not owned by the Marlins. It is also the longest affiliation in the team's history. Their newest affiliates are the Double-A Pensacola Blue Wahoos of the Southern League and the High-A Beloit Sky Carp of the Midwest League, which became Marlins affiliates in 2021.
Geographically, Miami's closest domestic affiliates are the Jupiter Hammerheads and Rookie Florida Complex League Marlins, which share a ballpark approximately 77 miles (124 km) away. Miami's furthest domestic affiliate is the Beloit Sky Carp some 1,259 miles (2,026 km) away.