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Diatom composition of the rheoplankton (phytoplankton) in the Sajó- Hernád river system (Slovakia and Hungary) was studied. Forty two sample sites were designated on the watershed from source to mouth of the two rivers and their tributaries. Samples were taken in July 2012. Altogether, 258 diatom taxa were identified. The microflora was dominated by tychoplanktonic elements. According to the relative abundance of the occurring taxa, four groups could be distinguished. Differentiation of these groups was confirmed by differences in the habitat characteristics, viz. altitude, width of watercourse, macrophyte coverage and river bed material. Diversity of diatom taxa in the phytoplankton was also studied. A positive relationship was found between the macrophyte coverage and the Simpson and the Shannon indices. In contrast, a negative relationship was shown between the macrophyte coverage and Berger-Parker diversity, in which metric the role of the dominant taxa is emphasized. Although the phytoplankton in rhithral rivers is influenced by stochastic events, our results reveal that geographical and hydromorphological characteristics of the rivers and coverage of macrophytes can also play role in shaping the composition and diversity of the phytoplankton.