Chrysophyllum gonocarpum is a tropical tree species that is very important in the recovery of heterogeneous forests and of degraded areas of permanent preservation. We identified microsatellite loci for C. gonocarpum to assess the genetic variability and the patterns of the population structure of the species. We isolated 8 microsatellite primers by using CT- and GT-enriched genomic libraries. We detected 2-4 alleles with 2.9 alleles per locus on average, by polymerase chain reaction. Test for cross-amplification showed that some loci were successfully amplified in 2 other Chrysophyllum species. The microsatellites can be used to assess the genetic diversity and population structure of C. gonocarpum. Some primer pairs can be amplified in C. marginatum and C. splendens.