In the framework of the international project EMERGE, species composition of epilithic diatoms of 34 selected high mountain lakes of Slovak part of the Tatra Mountains were investigated. In all, 127 taxa of diatoms belonging to 26 genera were recorded. Comparison of the epilithic assemblages of the investigated lakes showed differences both in relative abundance and taxa present in the individual lakes. On the basis of species composition and relative abundance of epilithic diatoms using hierarchical cluster analysis, two main groups of lakes were created. The first group includes 4 lakes which can be classified as strongly acidified and 9 lakes which are acidified or threatened by acidification. In this group, acidophilous species such as Achnanthes helvetica, A. marginulata, Aulacoseira distans and Tabellaria flocculosa prevailed. The second group includes 19 non-acidified lakes. The most common diatoms in these lakes were Achnanthes minutissima, A. helvetica, Cymbella minuta and Denticula tenuis which occur practically in all these lakes but with different abundances. The division of lakes due to their diatom species composition mostly confirmed the status of these lakes as judged from their water chemistry.