In highly mobile philopatric species, defining the scale of natal homing is fundamental to characterizing population dynamics and effectively managing distinct populations. Genetic tools have provided evidence of regional natal philopatry in marine turtles, but extensive sharing of maternally inherited mitochondrial control region (CR) haplotypes within regions (<500 km) often impedes identification of population boundaries. Previous CR-based analyses of Florida (USA) green turtle Chelonia mydas nesting sites detected at least 2 populations, but the ubiquity of haplotype CM-A3.1 among southern rookeries decreased the power to detect differentiation. We reassessed population structure by sequencing the mitochondrial microsatellite (short tandem repeat, mtSTR) in 786 samples from 11 nesting sites spanning 700 km from Canaveral National Seashore through Dry Tortugas National Park. The mtSTR marker subdivided CM-A3.1 into 12 haplotypes that were structured among rookeries, demonstrating independent female recruitment into the Dry Tortugas and Marquesas Keys nesting populations. Combined haplotypes provided support for recognition of at least 4 management units in Florida: (1) central eastern Florida, (2) southeastern Florida, (3) Key West National Wildlife Refuge, and (4) Dry Tortugas National Park. Recapture data indicated female nesting dispersal between islands <15 km apart, but haplotype frequencies demonstrated discrete natal homing to island groups separated by 70 km. These isolated insular rookeries may be more vulnerable to climate change-mediated nesting habitat instability than those along continental coasts and should be monitored more consistently to characterize population status. Broader application of the mtSTR markers holds great promise in improving resolution of stock structure and migratory connectivity for green turtles globally.