Zoo and aquarium breeding programs rely on accurate pedigrees to manage the genetics and demographics of captive populations. Breeding recommendations are often encumbered, however, by unknown parentage. If an individual has any amount of unknown ancestry, the relationships between that individual and all other individuals in a population are ambiguous, and breeding recommendations cannot be tailored to maximize genetic diversity and minimize inbreeding. In those situations, breeding program management might be improved by the incorporation of molecular data. We developed microsatellite markers for the parma wallaby (Macropus parma) and investigated how genetic data might be used to improve the management of the captive population. The parma wallaby is a small marsupial found in fragmented forests near the coast of New South Wales, Australia. Because the species is of conservation concern, the captive population in North America is managed by recurring breeding recommendations. The effectiveness of the population's management is hampered, however, because over half of the individuals have some amount of unknown ancestry. We used microsatellite data to resolve unknown parentage, described how molecular estimates of relatedness might inform future breeding recommendations, and used computer simulations to investigate how molecular estimates of relatedness among founders might contribute to the genetic management of the population. Our results indicated that microsatellite appraisals of parentage were useful with respect to clarifying pedigrees but that molecular assessments of founder relatedness provided very marginal benefits with regard to the preservation of genetic diversity and the avoidance of inbreeding.