Studies describing the population genetic structure and breeding system of basal lineages of termite species remain rare. Such species, however, may reveal ancestral life history attributes potentially influential in the evolution of social life within the Isoptera. Through the development and application of microsatellite DNA loci, we investigated patterns of genetic diversity and differentiation within the dampwood termite Zootermopsis angusticollis collected from three geographically distinct locations in California, USA. Significant genetic differentiation was identified among all sites, which were located 40-150 km apart, and each site was found to represent unique populations with limited levels of gene flow. While Z. angusticollis alates have previously been described as being strong fliers, genetic evidence suggests limited dispersal, possibly due to habitat characteristics restricting long-range flights. Additionally, we characterize patterns of colony genetic structure and breeding system within both Z. angusticollis and its congener Z. nevadensis nuttingi. In Z. angusticollis, simple, extended, and mixed family colonies were observed. The frequency of simple families ranged from 16 to 64%, whereas mixed families were found in only two locations and at low frequencies. In contrast, Z. n. nuttingi, formed primarily extended family colonies. Estimates of relatedness suggest that monogamous pairs heading simple families consist of reproductives showing variable degrees of relatedness from unrelated to close relatives. Additionally, the effective number of neotenic reproductives appears to be low within extended families of both species.