The koala (Phascolarctos cinereus) is one of Australia’s most iconic marsupials that is currently under threat due to habitat fragmentation, disease and urbanisation. The major histocompatibility complex (MHC) is a set of cell surface proteins that are not only crucial for immunity but have also been found to play a large role in mate choice in many species. Characterising the MHC of the koala is fundamental to understanding resistance and susceptibility to common diseases such as Chlamydia and has important conservation implications. However, the large numbers of functional and non-functional MHC loci throughout marsupial genomes poses a great challenge to researchers wanting to study these genes. We discuss how third generation, long-read sequencing of the koala genome enabled efficient and accurate characterisation of the koala MHC. Further, we will discuss how the characterisation of these genes was utilised in downstream studies which investigated the role of MHC in chlamydial vaccine responses and koala mate choice. The results from these studies demonstrate the benefits of third generation sequencing technologies and the importance of the MHC in the conservation of an Australian icon.