Research works aimed at assessing the interaction in the host-parasite system, pay attention to the products of the vital activity of the parasite. Hemozoin is one of the most promising metabolites that can be used for new methods of parasite diagnostics and treatment. It is known that hemozoin is produced by parasites causing schistosomiasis and malaria. Recent research has shown that hemozoin is produced by the hepatic trematode Opisthorchis felineus, but the effects associated with the presence of hemozoin in the bile ducts of the host have not been studied yet. The authors compare the concentration of hemozoin in various organs of animals and study the ability of the O. felineus hemozoin to modify the bile ducts microbiota. The authors study the bile duct microbiota of infected and healthy animals and perform the metagenomics analysis. The microbiota is assessed by metagenomic analysis of bile duct samples of intact animals and animals with opisthorchiasis. Samples of mature forms of O. felineus are also included in the study. In accordance with the results obtained, hemozoin accumulates mainly in the liver during the invasion of O. felineus. The invasion of O. felineus leads to an increase in the alpha diversity of the bile duct microbiota in animals, and this effect is not associated with the presence of hemozoin in the bile ducts. Metagenomic analysis revealed that the most representative taxa in the mature forms of O. felineus are Sphingomonas, Prevotella, Methylobacterium.