Although salinity and aquatic biodiversity are inversely related in lake water, the relationship between types of salts and zooplankton communities is poorly understood. Further, there is no information on whether variation in salt concentration contributes to the genetic divergence of zooplankton populations. In my study, lake water dominated by chloride anions had distinct zooplankton communities from those dominated by sulphate/carbonate anions. This distinction likely resulted from the combined effects of contrasting water chemistries and predation regimes. Greater haplotype diversity and genetic divergence was observed among populations of halophilic Brachionus plicatilis than among populations of predominantly freshwater Keratella quadrata rotifers. The most divergent B. plicatilis population was a strain that was most abundant at lower salinities. I provide preliminary evidence for an additional sibling species in the B. plicatilis species complex. This study documents some of the first molecular phylogenetic work conducted on rotifers.