Bacteria play an extremely important role in the digestive processes occurring in the digestive tract of all vertebrates. A disturbance of microbial balance may lead to disorders in digestive processes. Due to the high demand for fish from aquaculture, many studies have focused on the microbiome of the digestive tract in these animals, especially synbiotic Lactobacillus bacteria, which play an extremely important and beneficial role in digestive processes. Research conducted in recent years has shown that many factors influence the microflora in fish, such as the surrounding environment, oxygenation, water temperature, food intake, antibiotics, chromium oxide, linoleic acid, and finally the development stage of the fish. The authors of the publication provide an overview of the current knowledge on the gastrointestinal microflora of Cyprinidae and its effect on their digestive processes. In this context information on the probiotic therapy in Cyprinidae was also presented