The invasion of bivalves by parasitic microalgae Coccomyxa is widespread and causes pathologies and dysfunctions of the organs, especially in the most valuable products: the mantle and the muscle. The pathogenesis of the disease remains completely unknown. In this study, based on a macroscopic examination of Modiolus kurilensis and microalgae count in each infected individual, four stages of disease development with characteristic pathognomonic symptoms were described. During the progression of the disease, the concentration of alkaline phosphatase, glucose, calcium, hemolytic and agglutinating activities, number of basophils, eosinophils, phagocytes, and cells with reactive oxygen species increased in the hemolymph, while number of agranulocytes, cells with lysosomes, dead hemocytes, total protein concentration, as well as the weight of mollusks decreased. In the nephridia and digestive gland, necrosis, invasion of Nematopsis sp., hemocyte infiltration, and fibrosis increased. The ratio of changed tubules and occurrence of granulocytomas increased in the digestive gland, while the base membrane, nephrocytes and concretions changed in the nephridia. This study helps establish the variability of these parameters under normal conditions and their alteration during the disease. Moreover, these findings can be used for veterinary monitoring of the state of bivalves in natural and aquaculture populations.