We have constructed the first genetic linkage map for the North American arboviral vector Culex tarsalis. 120 F(2) offspring from a cross between two colonies were genotyped using 25 microsatellites and six inter-simple sequence repeat (ISSR) markers. We resolved four linkage groups which likely correspond to two full-length chromosomes and two arms of the final chromosome. The longest linkage group contains the sex locus and corresponds to chromosome 3. Recombination rates around the sex locus were dramatically higher in females compared to males. The majority of microsatellite loci share sequence identity with regions of the Culex quinquefasciatus genome, whose assembly should aid in anchoring linkage groups to physical chromosomes. This map will aid in identification of loci involved with variable phenotypes in C. tarsalis including WNV susceptibility.