The animal-mediated pollination and seed-dispersal mutualisms of Ficus species give them key roles in tropical ecosystems, but may make them vulnerable to habitat fragmentation. The development of highly polymorphic markers is needed to analyse their genetic diversity and investigate the effects of fragmentation on gene flow. Of thirteen microsatellite loci isolated from Ficus insipida, a monoecious species in French Guiana, eleven were polymorphic (two to six alleles each). High levels of variation were found among loci; expected heterozygosities ranged from 0.151 to 0.715. All markers revealed a broad cross-species affinity when tested in 23 other Ficus species.