We present an ecological history of the koala (Phascolarctos cinereus) population and its environment in South Gippsland, Victoria, both pre-and post-European settlement. We consider the role that the region's history may have had on the genetic structure of the current koala population in South Gippsland, which is the only known koala population in Victoria that does not originate from animals reintroduced as part of the Victorian translocation program. Following European colonisation of Australia, a range of anthropogenic factors, including hunting for the fur trade, resulted in widespread population declines for the koala. In Victoria, the situation was extreme. Currently, many koala populations in Victoria are derived from only a few individuals which existed less than 120 years ago. These populations therefore have comparatively low genetic diversity, a factor that plays a key role in long term population viability. In Victoria, the koala is not listed as a threatened species. Despite the low genetic diversity of most populations, the species is widely distributed across the state, and relatively common. Indeed, some populations are considered overabundant. However, many koala populations are not abundant, and population data are lacking for most. The South Gippsland koala population is of high conservation significance as it has greater genetic diversity compared to other Victorian populations, though there is little additional data to inform its conservation. An improved understanding of genetic diversity and gene flow between populations across the koala's range is required to guide the conservation of genetic diversity in this species. Monitoring population size, health and genetic relationships both within and between koala populations will enable better conservation outcomes.