Rapid urbanization in southern California has resulted in great amount of habitat loss for the organisms in the area. Among the small mammals that inhabit the area, much of the attention has been given to kangaroo rats, Dipodomys. But information regarding their sister taxa, pocket mice (both Chaetodipus and Perognathus) has been largely neglected. In this study, four populations of California pocket mice (Chaetodipus californicus) were captured and studied. First, foothills of Los Angeles and San Bernardino Mountains were surveyed using live capture traps. Second, microsatellite genetic markers were developed. Finally, population genetic data were accumulated using the microsatellites.

Total of 50 individuals of C. californicus were captured (C.c.bernardinus - 28, Cc.dispar - 22). Nine species specific microsatellite genetic markers developed and submitted to GeneBank. Among them, two were monomorphic, and two revealed excessive polymorphism. H_E ranged from 0.540 to 0.958, and H_O ranged from 0.000 to 0.740. Number of unique alleles ranged from 0 to 3. F _ST, F_IT, and F_IS were 0.04758, 0.53702, and 0.51389, respectively. Although these four populations consisted of two different subspecies of C.californicus, test for population differentiation showed that they were single unit half of the time, and two distinct units one third of the time.

Since there were only five microsatellite loci screened for the analyses, result is limited in understanding the overall genetic fitness of the organisms, indication of genetic differentiation among populations were minimum. Trapping effort involving more sites, especially around the contact zones of subspecies, should proceed to further increase our knowledge base for the organism.