Maintaining the genetic diversity of threatened populations is essential to preserving species’ adaptive potential. We can use studies of immunogenetic diversity in natural populations to learn how evolutionary processes affect key genomic diversity. This data allows us to refine management methods to maximise diversity, with the aim of maximising the long-term genetic health of the population. We are using measures of immunogenetic and genomic diversity, alongside pedigree-based mean kinship methods, to aid in the conservation of Tasmanian devil. Devil populations in the wild are gravely threatened by a contagious cancer, so in 2006 an “insurance population” was established across zoos and reserves to protect the species from extinction. Our work examines how genetic diversity of the insurance population is being preserved, and tests whether current approaches can be improved. Although this work is in the early stages, we demonstrate how the latest sequencing, analytical and computational methods allow us to test the role of evolutionary processes on maintaining immunogenetic diversity and fitness. These results will aid not only Tasmanian devil conservation, but also provide a greater understanding of the assumptions underlying conservation management strategies for all species.