The strict limitations on the fishing quotas for Atlantic cod (Gadus morhua) have meant the European flounder (Platichthys flesus) has become the third most commercially fished species in the Baltic Sea. Recent reports from the International Council for the Exploration of the Sea and local fishermen, however, indicate a noticeable decline in the fitness of the species and catch volume in the Baltic Sea over the last decade. As the alimentary tract is one of the major entry routes for toxicants and parasites, and since any disturbances in its functioning are directly responsible for harmful changes in the health and welfare of the fish, a diachronic examination of the digestive tract of the European flounder sampled from the Slupsk Bank was carried out in order to determine possible factors behind the observed detrimental changes in its success in the Baltic Sea. The results obtained revealed a serious Glugea stephani infection and the presence of microsporidiosis in the fish studied (a prevalence of 41.9 % and a mean infection intensity of 9.15 xenomas per fish) considerably higher than those previously reported in less polluted regions studied across Atlantic and Pacific. This may suggest the influence of factors conducive to improving the success rate of the invading parasite, such as an increased level of environmental pollution and oxygen deficiency on the sea bottom, both of which contribute to a greater density of fish in a limited area. Our study indicates the need for comprehensive parasitological investigation of the European flounder in the Baltic Sea, in order to study microsporidiosis and the level of parasitic infection detected in histopathological and molecular analyses, including metacercariae of Zoogonoidae, nematodes of Cucullanidae, Anisakidaea and Parafilaroides normani. This study detected Parafilaroides normani, hitherto unknown in Europe, with a probability of 91.41 %.