Disentangling the relative influence of historical versus contemporary processes shaping the spatial distribution of genetic variation is critical if we are to effectively mitigate key biodiversity issues. We utilize a comprehensive approach based on different molecular marker types and analytical methods to understand the demographic consequences of recent habitat fragmentation in a spatially explicit context. We focus our efforts on native leaf-toed geckos (Phyllodactylus tuberculosus saxatilis) throughout fragmented habitat in the tropical dry forest of northern Mexico as recent evidence suggests that geographic ranges for these geckos may be much smaller than currently realized. However, no data are available regarding recent shifts in demographic trends and how these trends may correspond with recent fragmentation and introductions of non-native gecko species (Hemidactylus). Mitochondrial DNA sequences reveal substantial historical genetic divergence over a small geographic area (<40 km). We find evidence for an increase in contemporary versus historical migration rates based on 10 microsatellite loci, but evidence that many populations suffer from recent reductions in effective population sizes. Landscape genetic analyses find that contemporary migration rates are significantly more correlated with the landscape versus historical migration rates or mtDNA divergence, suggesting that individuals have altered their dispersal routes in response to recent habitat changes. Taken together, this study suggests that long-term female philopatry, recent habitat fragmentation, and possibly introductions of non-native gecko species all contribute to the demographic patterns and the high degree of differentiation observed over fine-spatial scales in Mexican leaf-toed geckos.