Corridors of natural habitat are often sought to maintain dispersal and gene flow among habitat patches. However, structural changes in natural habitat over space and time may influence connectivity. Here we investigate whether differences in forest structure and the frequency of potential retreat sites is associated with the genetic structure of a tree-dwelling Australian gecko (Gehyra variegata). We sampled 113 adult geckos from multiple state forest and adjacent reserve locations within the Pilliga forest, New South Wales, Australia. Individuals were genotyped at 14 microsatellite loci and levels of dispersal were inferred by the degree of genetic structuring observed in state forest and reserve. A greater proportion of dead trees and tree debris (features that are used as retreat sites by G. variegata) were present within the state forests than in the reserve locations (P<0.05). This reduction in frequency of retreat sites in reserves was associated with significantly less genetic structuring of G. variegata, implying higher levels of dispersal. Tail loss was also significantly higher in G. variegata sampled in reserves than in the state forests. We conclude that dispersal characteristics in G. variegata are associated with structural changes to natural habitat and that this may influence rates of predation.