The ability of a selected strain of the malaria vector Anopheles gambiae to encapsulate the early oocysts of the malaria parasite Plasmodium cynomolgi B has previously been shown to be genetically linked to specific esterase phenotypes. This association between Plasmodium susceptibility and esterase phenotype is found in the An. gambiae G3 strain from which the Plasmodium-refractory and -susceptible mosquio strains were derived. Genetic crosses had suggested that the esterase phenotypes reflect the assortment of two alleles at one esterase genetic locus, with the two esterase homozygotes showing Plasmodium-susceptible and -refractory phenotypes and the esterase heterozygote being intermediate in susceptibility. By using a variety of specific esterase inhibitors in conjunction with esterase staining of gel-electrophoresed mosquito homogenates, we found that the bands previously thought to reflect one genetic locus are actually the product of two different esterase loci, Est1, a cholinesterase, and Est2, a carboxyesterase. In addition, examination of chromosomal inversions and the esterase phenotypes in the An. gambiae G3 strain revealed that different forms of a polymorphic inversion on the left arm of chromosome two (the 2La inversion) are inseparably associated with different alleles at these two esterase loci. We conclude that the genetic association among the esterase-linked Plasmodium-susceptibility locus and the two esterase loci is maintained by the suppression of recombination in 2La inversion heterozygotes in the An. gambiae G3 strain and its selected derivatives.