Over the last 15 years, the Australopapuan marsupial sugar glider (Petauridae: Petaurus breviceps) has become popular throughout the world as an exotic pet species. Here we present an investigation of genetic diversity, based on multilocus microsatellite genotypes and DNA sequence data, in a sample of 80 pet sugar gliders from South Africa. Our objectives were to infer the source region of these gliders, to estimate the effective size of the South African pet population, as a proxy for the number of founders, and to ascertain the risk of inbreeding depression in this captive population. Phylogeographic analysis of sequences from mitochondrial (ND2 and ND4) and nuclear loci (Omega Globin) suggests that the founders contributing to this sample were obtained from at least two distinct wild populations. The estimated effective population size is close to our sample size, implying that many founder individuals were imported into South Africa. Diversity within the captive population is high relative to that recorded from wild populations in Australia, consistent with admixture of founders from diverse and divergent sources. Although relatedness and inbreeding coefficients vary substantially among groups, there is low risk of inbreeding depression if breeders avoid mating close relatives. We discuss these results in the context of global trade in sugar gliders and the sustainable management of recently established captive mammal populations.