Introduction. One of the frequent complications of the type 2 diabetes mellitus (T2DM) is a metabolic-associated fatty liver disease (MAFLD). Aim. To study the composition of gut microbiota in patients with a combination of T2DM and MAFLD and to compare it with the microbiota in isolated T2DM and MAFLD. Methods. 111 patients were studied. The main group consisted of 56 patients with a combination of MAFLD and T2DM; the 1st group included 28 patients with MAFLD and the 2nd - 27 patients with T2DM. The control group consisted of 30 practically healthy people. Diagnosis was made by steatometry, shear wave elastography, lactulose H2 breath test, qPCR of feces using primers targeting the 16S rRNA gene, and stool culture. Results. In the the main group SIBO was found in 48.2%, in 1st – 35.7%, in 2nd – 33.3%, compared to 10% in the control group. When compared with healthy people, the number of "other" microorganisms significantly increased in the group with isolated T2DM and Clostridium, Proteus and Candida were cultured; in the case of isolated MAFLD, a decrease in Bacteroidetes and an increase in the Firmicutes/Bacteroidetes ratio, as well as an increase in Klebsiella and Clostridium. In the main group, an increase in Actinobacteria, "other" microorganisms, a ratio of Firmicutes/Bacteroidetes and a decrease in Bacteroidetes were found, when cultured - an increase in Clostridium, Klebsiella and Candida. Conclusions. Only the group of MAFLD with T2DM was characterized by increased Actinobacteria; decreased absolute number of Bifidobacterium and Lactobacillus and increased Escherichia, including with altered enzymatic properties in the stool culture.