The present work gives the results of the research of macrozoobenthos some running waters drainage areas of the Dyje River (southern Moravia – Czech Republic). Altogether, 762 taxa of macrozoobenthos were determined from the running waters of southern Moravia. Porifera (3), Hydrozoa (3), Turbellaria (8), Nematoda (14), Nematomorpha (1), Oligochaeta (60), Hirudinea (18), Bryozoa (5), Mollusca (44), Isopoda (2), Amphipoda (4), Decapoda (2), Hydracarina (17), Ephemeroptera (65), Plecoptera (55), Odonata (26), Heteroptera (3), Plannipennia (2), Trichoptera (128), Coleoptera (59), Diptera (243). Some taxa of macrozoobenthos are extinct unfortunately in running waters of Southern Moravia at present time. Another ones appear newly, for example snail Potamopyrgus antipodarum from New Zealand or Dreissena polymorpha from Pontic region. The data presented in this paper may serve as a basis for future monitoring of water quality and zoobenthos composition in connection with presumption of climate changes.