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Nearly complete 28S rRNA gene sequences newly obtained for 7 macrodasyid and 2 chaetonotid gastrotrich species, including one Neodasys species, as well as 18S rRNA gene sequences for 2 macrodasyid species were integrated into the set of 81 gastrotrich and 5 flat worm sequences. Both Bayesian and ML analyses display phylogenetic trees with well distinguished monophyletic Macrodasyida and Chaetonotida and Neodasys at the base or within macrodasyid group, depending on absence or presence in analyses of Cepalodasys and Urodasys sequences. Within Macrodasyida sequences of species from families Turbanellidae, Dactylopodolidae, Thaumastodermatidae and Macrodasyidae but not Lepidodasyidae form monophyletic groups. Within Chaetonotida only families Xenotrichulidae and Dasydytidae form monophyletic groups, whereas Chaetonotidae seems to be polyphyletic. All forced topologies with Neodasys at the base or within Chaetonotida are significantly worse by Bayesian criterion compared to topology with Neodasys at the base of Macrodasyida (Table1). The results obtained exhibit monophyly of the Gastrotricha with two well distinguished groups Macrodasyida and Chaetonotida and with Neodasys at the base or within Macrodasyida.