The koala (Phascolarctos cinereus) is an iconic Australian species with complex management requirements, from halting declines to dealing with overabundance. The discrepancy in population trends across their distribution means that broad scale management of koalas is not ideal. 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 of 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 sequencing methods (targeted exon capture) to develop a single nucleotide polymorphism (SNP) assay for use in koala population genetic studies at a range of scales, from individualization within local and captive populations to broad scale population genetics. Identified neutral and functional SNPs will allow us to investigate gene flow and neutral genetic diversity across the koala’s distribution as well as through time with both contemporary and historic museum samples to be analyzed. Additionally, as part of the Koala Genome Consortium, these SNPs have been mapped 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 of this species.