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Zooplankton and meiobenthos invertebrates of the Putorana Plateau are very poorly studied. In samples collected from three different altitudinal zones, 72 zooplankton, 28 meiobenthic Harpacticoida species and 11 meiobenthic macrotaxa were identified. Among them, 18 species were new to the Putorana Plateau, and one species was new to science. Three altitudinal zones were significantly different in the composition of invertebrate taxocenes. Zooplankton species richness decreased with altitude, while meiobenthic taxa richness increased. Altitude, water temperature, mineralisation and flow intensity had the greatest influence on the differences between taxocenes.