Conservation breeding programs, such as fenced reserves, conserve species by removing populations from key threatening processes and providing supplementary resources to support species preservation. This form of management often has the eventual aim to reintroduce individuals back to their native habitat. A key issue with captive management is the small breeding pool, due to generally small population sizes and limited migration, which may lead to inbreeding and consequent inbreeding depression. We investigated inbreeding and its potential fitness consequences in a large, free-ranging, captive population of an Australian marsupial, the long-nosed potoroo (Potorous tridactylus), a species that has been recently impacted by severe bushfire. We used reduced-representation sequencing to genotype single nucleotide polymorphisms and reconstruct a pedigree for the population. We detected low levels of inbreeding in our partial pedigree that incorporated 50.7% (34/67) of sampled individuals. Inbreeding depression was investigated using heterozygosity–fitness correlations of six fitness measurements, but we found no evidence of inbreeding depression in the population despite strong molecular evidence for inter-individual variation in inbreeding coefficient. Our findings suggest that the potoroo population at Tidbinbilla Nature Reserve (TNR) maintains a high level of diversity. As the population is descendant of animals from divergent sources, the TNR population also helps conservationists to learn more about potential consequences of admixture, and plan recovery strategies for the species. For TNR potoroos, we suggest that current management protocols have been effective at maintaining diversity to date. More generally, our results show how modern molecular techniques can efficiently characterise the genetic profile of a free-ranging, captive population to help inform management guidelines for wild recovery.