Allozyme polymorphism investigation was performed with the aim to evaluate some population genetic characteristics of two species, Daphnia atkinsoni Baird, 1859 and Daphnia bolivari Richard, 1888 (Cladocera: Daphniidae), of temporary aquatic habitats in the Hungarian Great Plain. The analysis showed that D. bolivari is not a distinct taxon, but is nested within D. atkinsoni. At the same time, remarkable within-species differentiation was revealed in D. atkinsoni; two presumable cryptic lineages were detected by our enzyme polymorphism investigation. The separation of the lineages is mainly due to the allozyme pattern at the AAT locus. Multivariate analysis of abiotic variables of the sampling sites revealed the relation between the genetic and ecological data, pH being the relevant variable explaining 81% of the genetic variability