Animals with deformed shells and microalgal invasion have been identified in the natural population of the horse mussel species Modiolus kurilensis of Peter the Great Bay in the Sea of Japan. The haemolymph is initially infested with algae, followed by the rectum, siphons, mantles and gonads located in the posterior body areas. Mantles, which are primarily exposed to light, are major depots for algae. The microscopic analysis of algal cells has revealed the absence of flagella and pyrenoids, the presence of single chloroplast, and reproduction by autosporulation, with dispores prevailing over tetraspores. These results, together with the nearly complete sequence analysis of small subunit (SSU) 18S rDNA (1728bp), have confirmed that these cells are Coccomyxa parasitica. A newly developed method of isolating microalgae from mollusk tissues has facilitated the continuous pure - probably axenic - culture of C. parasitica, thereby providing a description of the time course of each life stage. Histological analyses have revealed significant haemocyte infiltration into the mantles, gonads, kidneys and digestive gland tissues infested with microalgae and the gill tissues, in which the intruder was not identified. Algal encapsulation with major focal areas of fibrosis and amorphic necrosis has been revealed in these infested organs. The spaces between the gonad follicles and digestive gland tubules were significantly widened as these areas were filled with a mass of algae and phagocytic haemocytes, showing acini with a thickened basement membrane. The mantles and kidneys of Modiolus displayed significant morphological deviations of different cells in epithelial, connective and muscle tissues, resulting in the dysfunction of the infested organs. Therefore, C. parasitica, which reproduces in the culture, regardless of the host, is a facultative parasite, causing major pathological alterations, such as anomalous histomorphological patterns and infested organ dysfunctions.