the cladocerans are important components of planktonic and benthic freshwater and good indicators of the trophic state of water bodies. the morphological taxonomy of many species of cladocera is considered complex with minor differences separating some species. nowadays, molecular techniques provide a powerful tool to identify and classify different taxonomical levels, using mainly ribosomal rna genes (rrna) as molecular markers. in the present work we performed pcr-rflp to separate ceriodaphnia dubia, an exotic species in brazil and the native species ceriodaphnia silvestrii, widely distributed in brazilian freshwater. the rflp analysis of the its1-5.8s-its2 region of rrna genes showed to be different between c. dubia and c. silvestrii when using enzymes ecori, apai and sali. thus, the its1-5.8s-its2 region proved to be a useful molecular marker to differentiate the studied ceriodaphnia species, which makes the task easier of telling apart species that are morphologically very similar. also, this methodology might be interesting in determining the distribution of the exotic species c. dubia in brazilian freshwaters, particularly in cases when c. dubia occurs in the absence of c. silvestrii, a particularly difficult task for ecologists who are not taxonomy specialists.