Ex situ conservation management remains an important tool in the face of continued habitat loss and global environmental change. Here, we use microsatellite marker variation to evaluate conventional assumptions of pedigree-based ex situ population management and directly inform a captive lowland tapir breeding program within a range country. We found relatively high levels of genetic variation (Ntotal = 41; mean HE = 0.67 over 10 variable loci) and little evidence for relatedness among founder individuals (Nfounders = 10; mean relatedness = -0.05). Seven of 29 putative parent-offspring relationships were excluded by parentage analysis based on allele-sharing, and we identified two individuals of high genetic value to the population (mk ≤ 0.007) that would otherwise have been excluded from the breeding program. Traditional assumptions of founders being unrelated and individuals of unknown origin being highly related led to overestimates of mean kinship and inbreeding, and underestimates of gene diversity, when compared to values found when genetic markers were used to inform kinship. We discuss our results within the context of recent studies that have assessed the utility of neutral molecular markers for ex situ conservation.