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Apicomplexan protists, such as Toxoplasma, Eimeria, Plasmodium and Cryptosporidium, are intensively studied as agents causing human and animal diseases. But less is known about lower apicomplexans, e.g. protococcidians and blastogregarines, inhabiting marine invertebrates and appearing to be very important in the comprehension of evolutionary pathways and phylogenetic relations within phylum Apicomplexa. The blastogregarine Siedleckia nematoides inhabits intestine of the littoral polychaete Scoloplos armiger. The elongated and flattened gamonts possess smooth surface lacking any grooves or folds and perform nematode-like movement. The pellicle appears trilaminar and underlain by longitudinal microtubules. Parasite is attached to the host cell via mucron: feeding mode is apparently myzocytosis. There are two morphotypes corresponding to macro- and microgamonts. Gamonts of protococcidian Eleutheroschizon duboscqui were often found in the same worms together with S. nematoides. The helmet-shaped parasites attached to the host cell show some metabolic activity; detached spindle-shaped individuals are more motile. Uni- and multinuclear cells (macro- and microgamonts) were found. The gamonts are covered by a parasitophorous sac. The surface of parasite exhibits shallow grooves with micropores at the bottom. The cortex seems trilaminar, consisting of poorly defined membranes and underlain by longitudinal microtubules. The complicated attachment apparatus consists of several short and thick projections arranged in circle surrounded by another circle of numerous fascicles of filaments. No organelles of apical complex were found. Both E. duboscqui and S. nematoides cannot be unequivocally characterized by the molecular phylogenetic analysis used in this study. Using the NJ method, E. duboscqui sequence forms a basal branch to Coelotropha-Aggregata lineage. However, by ML method this parasite appears unexpectedly affined to colpodellids, not to Sporozoa, as it could be assumed on morphology. S. nematoides has also unclear position on the phylogenetic trees: it affiliates either coccidians or gregarines depending on both a method and taxonomical sample. According to molecular data we can suppose that there could be several early emerging branches of Apicomplexa: existence of two classical branches (Coccidia and Gregarines) cannot be reliably supported by SSU RNA phylogeny. The recent molecular data, including other genes, are insufficient to verify this hypothesis.