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Mountain lakes have special importance in the neo- and palaeolimnology. The diatom flora of mountain regions of Europe has been studied in detail, but less attention was paid to the Romanian part of the Carpathians. Siliceous algae of mountain lakes (1,740–2,122 m a.s.l.) were studied in the Retezat Mts (South Carpathians, Romania). Sediment samples were collected in the deepest points of twenty-three pristine lakes between 2011 and 2014. A total of 152 species and intraspecific diatom taxa were found during this study (excluding the representatives of the two most diverse diatom genera Eunotia and Pinnularia). Altogether 140 taxa were listed and nomenclaturally checked from the previously published results. 79 common species and some rarely reported taxa are illustrated by means of light- (LM) and scanning electron microscope (SEM), and 40 other are presented here only with LM images. A partial diatom checklist is presented with 217 items, 80 of them have been recently recorded for the Retezat Mountains. This compilation focuses on small celled (< 20 µm) diatoms. The main aim is to help the identification to the hardly visible, lightly silicificied and recently described forms, instead of repeating the earlier published data. This guide consists of a detailed light and scanning electron microscopy documentation of the diatom flora, based on 752 LM and 188 SEM pictures. New Humidophila and Staurosira taxa are presented and a new combination is proposed for Achnanthes helvetica var. minor. The detailed, illustrated guide hopefully will be a useful manual for ecological and palaeoecological surveys in the future.