The koala (Phascolarctos cinereus) is an iconic Australian species with a complex management history. In the northern parts of their distribution, koala populations are in decline, primarily as a result of habitat loss and fragmentation, as well as disease (chlamydia and koala retrovirus (KoRV)). Conversely, in southern parts of their distribution, some koala populations are overabundant and require fertility control measures to manage numbers. The discrepancy in population trends across their distribution means that broad scale management of koalas is not an ideal strategy. Instead, management often occurs at local scales (in local government areas or on regional populations) with little reference to the broader Australian context. Previous population genetic studies on koalas have been carried out using a range of different marker sets. These are useful in isolation, but are often not comparable across studies. This study uses next generation methods to develop a SNP assay for use in koala population genetic studies at a range of scales, from individualisation within wild and captive populations to broad scale population genetics. An exon capture method has been used to identify both functional and neutral SNPs. These SNPs will allow us to investigate geneflow and neutral genetic diversity across the koala’s distribution. Additionally, as part of the Koala Genome Consortium, we will also have the opportunity to map these SNPs to the Koala Genome, providing unprecedented power to investigate a range of questions involving traits under selection, linkage, and much more. It is our hope that these markers may be utilised in future population studies, and by other researchers and management bodies to facilitate more consistent and comparable data collection for conservation management.