The Island Night Lizard (Xantusia riversiana) is restricted to three of the Channel Islands off the coast of California, USA. Introduced species have profoundly affected the fauna and flora of the islands for over 150 years, but most of these non-native species have been recently removed from the islands. We measured the distribution of genetic diversity in Island Night Lizards across San Nicolas Island to assess the impacts of historical habitat change on effective population size, gene flow, and population divergence; to provide baseline data for monitoring; and to provide recommendations for habitat restoration. Circuit theory modeling of habitat permeability and field studies indicated that population structure and distribution are largely influenced by exceedingly rare movements across long distances through unsuitable habitat.