Population genetic patterns can be affected by a number of factors, including life history characteristics, behavior, and landscape features. The ability to identify patterns and correlations among these factors can be invaluable in managing populations, particularly in areas with ever increasing urbanization. While many genetic studies have incorporated these parameters as potential influences in genetic structure, they often focus on a single species, with the resulting data having limited applicability in a broader conservation context. Comparative studies of similar or related species may offer important evidence to refine assumptions that are often made about the genetic response of similar species to natural and anthropogenic factors. The current study investigated genetic patterns in Peromyscus californicus and Peromyscus fraterculus in San Diego, California. The two species are closely related and commonly occur in coastal sage scrub and chaparral habitats, often in sympatry. Samples were collected from five sites throughout the county and analyzed using 10-12 microsatellites. Genetic patterns were evaluated on both broad (county-wide) and fine (intrasite) spatial scales through use of standard diversity and differentiation metrics, Bayesian clustering analysis, and landscape modeling. The results indicated that similar levels of genetic diversity exist in these species. Subtle genetic structure was present on a broad scale for both species, but finer scale structure was evident only in P. fraterculus. Fine scale spatial genetic patterns also differed between the species, and may be related to differences in certain life history traits such as mating system and dispersal. Two subpopulations of P. fraterculus located on opposite sides of the road at Jamul were found to be genetically different, but landscape modeling was unsuccessful in establishing influence of the road or other specific landscape features on these genetic patterns.