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Mesozoa is one of the minor metazoan phyla whose phylogenetic position remains yet unclear. In traditional phylogenies, mesozoans are classified as intermediate between unicellular eukaryotes and multicellular animals. Molecular trees of 18S rRNA genes point to possible kinship of two mesozoan groups (Dicyemida and Orthonectida) with nematodes and myxozoans. Similarity of the dicyemidan and lophotrochozoan Hox genes allows to consider Dicyemida as secondary modified representatives of some groups of higher protostome animals. In this work, nearly complete 18S and 28S rRNA genes from two orthonectid and one dicyemid species were sequenced and analyzed together with set of homologous sequences from the major metazoan phyla using various taxa sampling. Bayesian tree inferred from initial set of sequences displays basal position of Acoelomorpha and Nemertodermatida among Bilateria, early split of Bilateria into Deuterostomia and Protostomia, split of Protostomia into moulting Ecdysozoa and nonmoulting Spiralia, as well as formation of the Lophotrochozoa clade. At this tree, all 3 Mesozoa species unite into statistically well supported robust clade placed within the Lophophorata group, close to the base of Annelida assemblage. All phylogenies with separate position of dicyemids and orthonectids are rejected by statistical tests using parametric bootstrap. Monophyly of Mesozoa is also supported by molecular synapomorphies found in sequences of 18 and 28S rRNA genes. Analyses with various sampling of annelid taxa revealed tendency to convergence of Mesozoa with annelid assemblage including Capitellida, Echiura, Sipuncula and Oligochaeta.