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Cladistic analysis of morphological characters suggest the Nematoda to be a sister group of the Gastrotricha. Conversely, recent analyses of 18S rRNA gene sequences place the Nematoda in a hypothetical clade of molting animals "Ecdysozoa", or cluster them with Chaetognatha, whereas the Gastrotricha represented by the specialized order Chaetonotida, are placed outside these groups. To resolve this controversy, we re-examined the relationship of the Nematoda with other taxa, using additionally the 18S rRNA gene sequence of Turbanella cornuta, a species from the gastrotrich order Macrodasyida. Depending on taxon sampling, the Nematoda and Gastrotricha moved from basal to apical position in the 18S rRNA trees,but only occasionally appeared as sister groups. The greatest number of apomorphies in 18S rRNA sequences shared with Nematoda was observed in Gnathostomulida, Chaetognatha, and "Ecdysozoa". However, these characters do not form a clearly distinguishable common synapomorphic complex, being randomly distributed among all these taxa. Thus, the 18S rRNA gene data do not support a close relationship of Nematoda with Gastrotricha.