Unionicola poundsi and U. lasallei are recognized as closely related, morphologically distinct species of water mites living in symbiotic association with the mussels Villosa villosa and Uniomerus declivus, respectively. However, results of a transplant experiment suggested that the morphological characters used to separate these species are plastic and are influenced by the host species in which these mites metamorphose. These results indicate that U. poundsi and U. lasallei are variants of the same species. To test the validity of these contrasting notions, the genetic structure of mite populations from Uniomerus declivus and V. villosa was compared. An examination of allozyme variation at 9 enzyme loci revealed a high degree of genetic differentiation between these host-associated populations, with mites from U. declivus and V. villosa being fixed for different alleles at 3 loci and exhibiting significant allele heterogeneity at 71% of their polymorphic loci. Coefficients of genetic similarity and genetic distance for mites from U. declivus and V. villosa were 0.36 and 0.95, respectively. The results of this study suggest that mite populations from U. declivus and V. villosa are genetically distinct and complement morphological data recognizing them as valid species.