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Analysis of primary and secondary structures of the 18S rRNA molecule reveal monophyly of some groups within the Chromadoria, namely Monhysterida,Desmoscolecida, Araeolaimida, Plectida, and Secernentea, that led to clarify phylogenetic affinities of its several key taxa (Axonolaimidae, Linhomoeidae, Plectidae, Comeosomatidae). The molecular features found allow to delimit Monhysterida and Araeolaimida s.str. The part of the tree containing the major secarnential node is now more detailed. Family Plectidae constitutes a sister taxon to the Secernentea, and Araeolaimida s.str. are realized as the closest relatives of the Plectidae+Secernentea clade. The 18S rRNA data of the desmoscolecide Tricoma for the first time supports the view that this aberrant group of marine nematodes shares the most recent ancestor with lineage leading to the Secernentea.