Abstract: Culex tarsalis is a highly efficient laboratory vector of West Nile Virus, and has been implicated as an epidemic vector in the field. Its distribution ranges across the western United States, coinciding with the distribution of several recent WNV outbreaks. While the ecology of this vector has been extensively studied, little is known about its genetics and population structure. Information regarding population structure would lay the foundation for future studies of the relationship between population genetic variation and observed geographic variation in WNV transmission. Inter-simple sequence repeat (ISSR) screening, in which regions between microsatellites are amplified, indicated that microsatellite motifs (AG)_n, (AC)_n and (CAG)_n are common in the Cx. tarsalis genome. Genomic libraries enriched for these repeats were generated. An additional library was enriched for the repeat (ATG)_n, which was not investigated by ISSR. ISSR-guided libraries were highly enriched for microsatellites, with library-specific enrichment rates ranging from 81-96%. Library ATG was not as highly enriched (41%). Out of 98 total sequenced clones, 79 contained microsatellites of which 77 were unique. PCR primers were designed for 55 loci. Initial efforts have identified 11 loci that amplify reliably and are polymorphic. A preliminary screen of wild individuals from Coachella Valley, California has revealed high levels of genetic variation, with 3 to 9 alleles per locus and heterozygosity ranging between 0.18 and 1.0. The application of these microsatellite markers to the genetic structure of Cx. tarsalis will be discussed.