There is a possibility of developing a pathological process in the body of fish in the conditions of high-tech industrial aquaculture and at high planting densities, creating chronic stress. Histological studies allow early detection of the initial stages of possible pathology at the cellular level. The studies have shown that apparently healthy individuals of African catfish grown in recirculating aquaculture systems (RAS) revealed pathology of cells and tissues of the gastrointestinal tract. They had edema of the internal muscle layer of the stomach and intestines, detachment of the epithelial layer from the gastric mucosa, violation of the structural organization of gastric fields on histological sections. Thinning of intestinal villus, reduction of their length and branching, violation of their structure up to destruction were also revealed. The study of the tissues of the stomach and intestines was carried out using a research motorized universal microscope Axio Imager.M2 (Carl Zeiss, Germany). To correct the pathological process, the experimental group of fish received a “sporothermin” probiotic with feed, which belongs to the probiotics of the last generation. It is an antagonist of a wide range of pathogenic and opportunistic microbiota and is used as an alternative to antibiotics. The composition of “sporothermin” includes spore forms of bacteria Bacillus subtilis and Bacillus licheniformis, which in the gastrointestinal tract of fish turn into vegetative forms. Bacteria Bacillus subtilis and Bacillus licheniformis are not representatives of the intestinal microbiocenosis of the African catfish, but they regulate its structure by reducing the level of pathogenic and opportunistic microbiota. Pathology of cells and tissues of the gastrointestinal tract have been identified in the fish of the experimental group treated with the sporothermin probiotic.