The ant genus Hypoponera, with its high diversity of alternative reproductive tactics, is of particular interest in studies on sexual selection. In the species Hypoponera opacior, winged and wingless males and queens co-occur and molecular markers are essential to study the reproductive success of these sexual tactics. Primers were developed for five polymorphic microsatellite loci isolated from H. opacior. Their variability was tested on 34 colonies from a population in the United States. Nine to 21 alleles per locus were found with observed heterozygosities between 0.1 and 0.7. A significantly positive FIS value suggests inbreeding in this ant with predominant intracolonial matings.