ABSTRACT. – The benthic microbial communities developing different substrata along the trophic gradient in Lake Balaton (Hungary) were analysed. Samples from north and south shoreline of three basins (Keszthely, Szigliget and Siófok) were compared based on 16S and 18S rDNA denaturing gradient gel-electrophoresis (DGGE) fingerprints. Composition of communities showed shift from June to August. Self-organizing map method (SOM) revealed a pronounced distinction of epipelon samples in the cases of both bacteria and eukaryotes. Besides, 16S rDNA-based patterns showed a separation of the northern and southern samples whereas the 18S rDNA-based results displayed the grouping of the basins with different trophic levels in August. Composition and diversity of benthic communities of different substrata were linked to chemical variables of the water column. Trophic gradient was mostly reflected in epipelon bacterial diversity changes. The 18S rDNA-based data showed that epilithon samples had low diversity.