Culex tarsalis is an important and efficient vector West Nile Virus in the western United States. Due to a lack of modern molecular tools, almost nothing is currently known about its population structure. We have developed a suite of mitochondrial and nuclear genetic markers to investigate the population biology of this mosquito. In analysis of a 389 bp fragment of the mitochondrial NADH dehydrogenase (ND4) gene, we found 39 different haplotypes circulating among California populations. Analysis of Molecular Variance (AMOVA) suggested that there is extensive gene flow and little population structure among California Culex tarsalis populations. Haplotype diversity and haplotype number neutrality tests indicated that while levels of haplotype diversity did not differ from those expected by chance, there were significantly greater numbers of haplotypes observed (i.e., a large number of rare haplotypes circulating in field populations). Comparisons between mitochondrial and microsatellite data will be discussed.