The habitat of the Critically Endangered western ringtail possum (Pseudocheirus occidentalis) has been greatly reduced and fragmented over time. There is a lack of information on small, remote populations of this possum, especially on the genetic diversity of isolated populations. To address these knowledge gaps, we generated thousands of genome-wide markers using next generation sequencing across the remnant range of the species. We used historical collections and opportunistically collected samples, to obtain genetic data for 305 samples across 23,146 loci. Overall, the three current management zones for this species explained the genetic diversity within the species relatively well, with some exceptions. We found evidence for eight genetically defined subregions - four population clusters in the Swan Coastal Plain, two contemporary clusters in the Southern Forest and two clusters in the South Coast. The findings from this work will contribute to recovery objectives for the western ringtail possum and assist with translocations for the genetic management of this species.