Islands are often acknowledged as a refuge for species with declining mainland distributions. However, as the finite size of islands coupled with isolation can lead to genetic deterioration within insular populations, the study of these systems is of great interest to the conservation of biological diversity and persistence. The remote Kimberley region in Western Australia is facing increased impacts from invasive species, habitat fragmentation, grazing, mining and altered fire regimes, and many of the 2633 islands in the Kimberley have come into focus as a significant conservation resource. The Barshouldered skink (Ctenotus inornatus) is a habitat generalist that is highly abundant throughout the Kimberley and its diverse islands. This study encompasses 41 islands and seven mainland populations in the vast Kimberley environment, and genetically characterises them using 18 nuclear (microsatellite) markers. The island populations lost heterozygosity at a rate of 1 % per kilometre from the mainland. Diversity was significantly lower on islands of small size (\500 ha) and greater than 2 km from the coastline. The scope of this study is unparalleled and addresses an important gap in our understanding of the genetic diversity throughout ecosystems. The findings illustrate how populations, operating within these pristine island systems, conform to the general rule of decreased genetic diversity with decreasing island area and increased distance from the mainland and identifies islands that may hold the most potential for conserving biodiversity.