Since its introduction in 1999, West Nile virus (WNV) has spread across North America. Culex tarsalis is a highly efficient WNV vector species. Many traits such as virus susceptibility, autogeny and host preference vary geographically and temporally in C. tarsalis. Culex tarsalis genomic libraries were developed and were highly enriched for microsatellite inserts (42–96%). We identified 12 loci that were polymorphic in wild C. tarsalis populations. These microsatellites are the first DNA-based genetic markers developed for C. tarsalis and will be useful for investigating population structure and constructing genetic maps in this mosquito.