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Zooplankton community data from 45 dimictic lakes, representing homogenous abiotic conditions, were used to distinguish indicator taxa of near-pristine, reference lakes with low anthropopression. Reference conditions were selected based on natural land use in the catchment, lack of or low human activity, and the absence of point sources of pollution, as well as good water quality. According to these criteria, six lakes were designated references and all represent mesotrophic conditions. Reference lakes had a low abundance of Cyclopoida and Rotifera, and significantly lower biomass compared to non-reference lakes. We have found that species characteristic of the reference lake were: <i>Bosmina</i> (<i>Eubosmina</i>) <i>coregoni</i>, <i>Ascomorpha ecaudis</i>, <i>Collotheca pelagica</i>, and <i>Gastropus stylifer</i>. The species responsible for differences among reference and non-reference lakes were <i>Keratella tecta</i>, <i>Pompholyx sulcata</i>, and <i>Ascomorpha saltans</i>, which are considered typical for eutrophic waters.