The mosquito Culex quinquefasciatus (Say) is a vector of human disease and a world-wide biting nuisance. Organophosphorus insecticides (OPs) have been widely used to control C. quinquefasciatus populations and this has led to the emergence of OP-resistance. Predominantly, resistance is caused by increased production of two non-specific carboxylesterases, Estalpha2(1) and Estbeta2(1). Increased abundance of these esterases is associated with the amplification of their respective genes. The estalpha21 and estbeta21 genes were cloned and sequenced from OP-resistant Sri Lankan C. quinquefasciatus; the two adjacent genes are in a head to head configuration, within a single amplification unit (amplicon). The homology between the two genes suggests that they arose from an ancient duplication event. The two genes have different numbers of exons (estalpha21 has seven and estbeta21 has four); however, the intron/exon boundaries in estbeta21 are all conserved in estalpha21. The two genes are co-amplified in three other mosquito strains with the elevated Estalpha2(1)/Estbeta2(1) phenotype. Their complete linkage disequilibrium is explained by the location of the two genes involved in resistance within a single amplicon. In insecticide-susceptible C. quinquefasciatus, the non-amplified estalpha and estbeta gene loci are also found in a similar head to head configuration, but the size of the intergenic non-coding region is approx. 1 kb less than in the amplicon. The smaller intergenic spacer is also found in a strain with amplified estbeta11, which suggests that extensive laboratory selection for this amplified esterase has not eliminated the non-amplified genes. The intergenic spacer regions have been subcloned and sequenced. They contain numerous possible TATA boxes, promoters and a number of possible regulatory elements with high homology to the consensus sequence of the Barbie box. These latter putative regulatory elements are more numerous in the larger intergenic spacer, which differs from the non-amplified spacer by two large (>>420 bp) and one small (5 bp) insertions.