A paramyxean parasite infection was observed in the epithelial cells of the stomach, intestine, and digestive diverticula of Manila clam Ruditapes philippinarum collected from Odawa Bay, Japan. The mean detection frequency between April 2010 and September 2011 as revealed by histology was 8.9% with a maximum monthly frequency of 28.6%, but remarkable mass mortality was not recognized during the study period. Sporulation of the parasites involves repeated production of intracellular cells, and a primary cell contains 8 secondary cells, in which 4 multicellular spore cells are produced. Several large eosinophilic granules formed in the cytoplasm of secondary cells during the final maturation process. Transmission electron microscopy (TEM) revealed that spore cells consisted of the innermost, intermediate and outermost cells, indicating that this parasite is a member of the genus Marteilia. TEM observations also revealed that the cell membrane of mature spores was lined with an electron-dense monolayer, which has not been reported from other species in the genus Marteilia. Determined SSU rRNA gene sequence of this parasite was apparently different from previously described Marteilia species, and this species was identified as Marteilia granula n. sp., a new species in the genus Marteilia, Order Paramyxida, Phylum Cercozoa. Our results identify for the first time the parasite species of the genus Marteilia infecting the Manila clam in Japan.