Marine environments are experiencing rapid warming, substantially altering ecosystems. Populations at the edge of a species’ range are more vulnerable to environmental change as they are first affected and may have limited dispersal opportunities. This vulnerability may be exacerbated in species with specialised foraging and breeding strategies. The Australian sea lion (Neophoca cinerea) is an endangered otariid species that breeds across a ~3000 km range in southern Australia. At the most north-westerly edge of the species’ distribution, Australian sea lions breed across multiple islands within the Houtman Abrolhos Archipelago, Western Australia, a tropical-temperate location affected by marine heatwaves. This study aimed to examine the genetic structure and diversity of the Australian sea lions from the Houtman Abrolhos Archipelago compared to other populations in the species’ range. One hundred and twenty-five individuals, nineteen from Houtman Abrolhos, were genotyped from nineteen sample sites across Western Australia and South Australia. Our findings showed that individuals from the Houtman Abrolhos grouped into a single population, which was highly differentiated and had extremely low genetic diversity. The isolation and limited genetic variation of the Houtman Abrolhos Australian sea lion population suggest that it is extremely vulnerable to extirpation. Our study highlights the vulnerability of isolated populations of a species to rapid environmental change and stochastic events.