Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. However, while threatened species management is generally the purview of state governments, intensive data collection at this scale is often neglected, despite arguably being the most useful for guiding ongoing conservation efforts. Using a proprietary genome complexity reduction-based method, we generated a data set of high-quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Genotyping of 314 individual koalas sourced from across the state of New South Wales was performed using the Diversity Arrays Technology platform (DArTseq™) with funding provided by the NSW Government under the New South Wales Koala Strategy (Grant Agreement No. KR_2019_01).

Our findings demonstrate that current management divisions across the state of NSW do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned amongst individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.