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Agamococcidians (Agamococcidiorida Levine, 1979) represent an enigmatic group of Apicomplexa. The life cycle of these parasites is characterised by presence of oocysts with sporocysts (similar to coccidian), sporozoites and trophozoites, and by absence of merogony and gamogony. This group combines two families Rhytidocystidae Levine, 1979, parasites of polychaetes, and Gemmocystidae Upton & Peters, 1986, parasites of stony corals. The phylogenetic position of these organisms is still unclear. Previous phylogenetic studies brought agamococcidians together with gregarines and cryptosporidians (Leander, Ramey, 2006; Rueckert, Leander, 2009; Kristmundsson et al., 2011; Cavalier-Smith, 2014). In contrast, morphological data (oocysts with sporocysts and nonmotile trophozoites located within host epithelial tissues) indicate a relationship of agamococcidians with coccidians. We isolated two putative new species of Rhytidocystis from polychaetes Pectinaria hyperborea and Ophelia limacina collected in the Keret Archipelago of the White Sea, Russia. The SSU rDNA sequences obtained from these new parasites clustered strongly with Rhytidocystis cyamus and R. polygordiae within the rhytidocystid clade. Phylogenies inferred from these sequences demonstrate a close relationship between rhytidocystids and marine coccidians. Interestingly, some coccidians closely related to rhytidocystids, such as Margolisiella islandica or Aggregata sp., have all three types of reproduction found among apicomplexans: sporogony, merogony and gamogony in their life cycles. Thus, our molecular data agree with known morphological data. We discuss the phylogenetic position and perspectives of further investigations of agamococcidians for more deep understanding of Apicomplexa evolution.