This pilot study presents surface sediment diatom assemblages in four alpine lakes in the Zelengora Mountains. The four lakes are distributed across an alpine treeline, spanning temperate mixed forest and treeless alpine tundra zones, thus offering an excellent opportunity to study the interaction of physicochemical properties and biotic communities in different alpine lake settings. A total of 52 taxa from 28 genera were identified, with only one taxon (Staurosirella neopinnata) present in every lake. In the Orlovacko, Donje Bare and Crno lakes, the diatom assemblages were mainly comprised of benthic and tychoplanktonic species, as opposed to the Kotlanicko Lake where the planktonic Lindavia radiosa was the most abundant species. Our results identified water turbidity, macrophytes and pH to be the prevailing environmental factors which influence the diatom assemblage composition in the studied lakes. The results of this study also represent a starting point in establishing biomonitoring programmes for the sustainable management of these alpine aquatic ecosystems in a rapidly changing environment.