A survey of 72 oligotrophic, clearwater high mountain lakes with minimum direct human impact in the Alps (Italy, Austria and Switzerland) was carried out in 2000 to identify biological indicators useful for lake classification. Samples were collected for water chemistry, phytoplankton, epilithic diatoms, littoral macroinvertebrates and zooplankton. Surface sediments were analyzed for algal pigments, metals, cladocera, chironomid and diatom remains. A multivariate analysis of morphometric, geographical and chemical variables identified two main gradients: (1) a geological gradient, from alkaline lakes in calcareous catchments to acidic lakes on granitic catchments, and (2) a morphological gradient including variables related to lake and catchment size and depth. The analysis of the biological data showed that the geological gradient is related to the composition of phytobenthos, as well as sedimentary diatoms and chironomids, while the morphological gradient is mainly related to the composition of algal pigments, phytoplankton and macrozoobenthos. The results were used to provide a lake typology for this ecoregion, and finally to identify indicator taxa. © 2009 E. Schweizerbart'sche Verlagsbuchhandlung, D-70176 Stuttgart.