Wild Iceland scallops Chlamys islandica from an Icelandic bay were examined for parasites. Queen scallops Aequipecten opercularis from the Faroe Islands and king scallops Pecten maximus and queen scallops from Scottish waters were also examined. Observations revealed heavy infections of eimeriorine parasites in 95–100% of C. islandica but not the other scallop species. All life stages in the apicomplexan reproduction phases, i.e. merogony, gametogony and sporogony, were present. Trophozoites and meronts were common within endothelial cells of the heart’s auricle and two generations of free merozoites were frequently seen in great numbers in the haemolymph. Gamonts at various developmental stages were also abundant, most frequently free in the haemolymph. Macrogamonts were much more numerous than microgamonts. Oocysts were exclusively in the haemolymph; live mature oocysts contained numerous (>500) densely packed pairs of sporozoites forming sporocysts. Analysis of the 18S ribosomal DNA revealed that the parasite from C. islandica is most similar (97.7% identity) to an unidentified apicomplexan isolated from the haemolymph of the giant clam, Tridacna crocea, from Japan. Phylogenetic analyses showed that the novel sequence consistently grouped with the Tridacna sequence which formed a robust sister clade to the rhytidocystid group. We propose the name Margolisiella islandica sp. nov., referring to both type host and type locality.