Physical features of the landscape as well as taxa-specific characteristics of an organism may shape population genetic patterns by affecting dispersal and gene flow. Understanding what affects population genetic patterns is critical for developing conservation management strategies. This is especially true in the changing landscape of anthropogenic habitat modification and global climate change. However, most conservation genetic studies focus on a single species in a particular landscape, thereby limiting the ability to attribute patterns to particular aspects of the species or landscape. To assess how landscape features may impact population genetic patterns in different species, I compared genetic diversity, divergence and landscape genetic patterns of two sympatric lizard species in multiple replicate sites. The western fence lizard (Sceloporus occidentalis) and the orange-throated whiptail (Aspidoscelis hyperythra, California Species of Special Concern) are small lizards that are abundant in the coastal sage scrub and chaparral habitats of coastal southern California. Lizard tissue samples were collected from five sites throughout San Diego County, California. A total of 325 samples of S. occidentalis were genotyped at 11 microsatellite loci, and 222 samples of A. hyperythra were genotyped at 10 microsatellite loci. Results suggest little fine-scale population genetic structure in these two lizard species. Analyses of the effect of roads on population genetic patterns vary by landscape site for both species. In particular, both lizard species at the site LOM show low genetic diversity and are susceptible to a barrier effect of the road. Analysis of pairs of first-order relatives reveals longer-distance dispersal events than previously reported for both species of lizard. Overall, the results presented here emphasize the importance of landscape features as well as taxa-specific ecological characteristics in shaping population genetic patterns. Both species- and site-specific approaches should be considered for future conservation genetic studies.