List of Miami Marlins minor league affiliates

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 mi away. Miami's furthest domestic affiliate is the Beloit Sky Carp some 1259 mi away.

Current affiliates
The Miami Marlins farm system consists of seven minor league affiliates.

1990–2020
Minor League Baseball operated with six classes (Triple-A, Double-A, Class A-Advanced, Class A, Class A Short Season, and Rookie) from 1990 to 2020. The Rookie level consisted of domestic and foreign circuits.

2021–present
The current structure of Minor League Baseball is the result of an overall contraction of the system beginning with the 2021 season. Class A was reduced to two levels: High-A and Low-A. Low-A was reclassified as Single-A in 2022.