The host immune response is an important factor determining the outcome of the host–pathogen–environment interaction. At the gateway between the innate and adaptive immune systems are MHC molecules, which facilitate antigen presentation to T lymphocytes, and initiate the adaptive immune response. Despite their integral role in adaptive immunity, the genes encoding class II MHC molecules have not been examined directly in koalas. Furthermore, indirect historical evidence suggests that this species might lack functional diversity in class II MHC genes, with potential implications for disease susceptibility. We have examined diversity in the β chain genes of the koala class II MHC DA gene family and identified 23 alleles, including several atypical alleles. The levels of diversity observed are consistent with other marsupial and eutherian species, and do not support the paucity of variation suggested by the early literature. These findings are relevant to the conservation management of koalas and provide both a benchmark for maintaining population diversity and a platform for further conservation genetic research in this species.