Genetic markers are a powerful tool to investigate the breeding structure and population genetics of subterranean termites. In this study, 10 - 20 subterranean termite workers, Reticulitermes flavipes (Kollar) were collected from colonies at 8 sites, separated by at least 200 m. Ten workers from each site were genotyped at 7 microsatellite loci. The data revealed that all 7 microsatellites were polymorphic with up to 6 alleles per locus. The frequency of most the common allele ranged from 0.11 - 0.60. Observed patterns of genetic variation within colonies revealed that most were the result of fusions of multiple colonies. Few colonies exhibited genetic variation consistent with a simple family headed by a single pair of reproductives. The analyses of F-statistics and relatedness coefficients indicated that the colonies were often inbred, suggesting they contained neotenic reproductives.