Comparative genetic differences for the phosphoglucomutase and trehalase loci were surveyed in larval and adult blackfly populations of the onchocerciasis vectors Simulium yahense Vajime and Dunbar, and S.sanctipauli Vajime and Dunbar. Genotype frequencies for each stage and all populations were at Hardy-Weinberg equilibrium, indicating that S.yahense and S.sanctipauli remain genetically distinct. S.yahense populations from three different locations were found to be genotypically comparable. The larval population of S.yahense found in closest proximity to a S.sanctipauli population was found to express the phosphoglucomutase allele 1.33, characteristic of S.sanctipauli, with significantly greater frequency than other larval populations of S.yahense. This may constitute evidence of limited genetic introgression of S.sanctipauli with the S.yahense population.