Recent advances in molecular and genetic research have illuminated the mechanisms of interaction between genes and the environment, which are partially mediated by so-called epigenetic modifications. These changes do not affect the primary structure of genes’ DNA, but cause persistent changes in their expression, which can be inherited by subsequent generations and determine the formation of the corresponding metabolic phenotype. Obesity, metabolic syndrome and type 2 diabetes mellitus develop on the basis of insulin resistance in the presence of a genetic predisposition under the influence of external factors, including environmental influences and lifestyle characteristics, in particular dietary habits. Today it has been proven that changes in the profile of intestinal microbiota is an important modifiable factor in the development of dysmetabolic states. Gut microbiota plays a key role in the regulation of many metabolic processes, inflammation, the activity of the immune system and the general state of the body. Diets enriched with fats and carbohydrates have been found to result in the decreased diversity and changes in gut microbiota composition, such as decreased levels of Bacteroidetes and increased Firmicutes. The accumulated data of clinical and experimental studies indicate a link between disorders in the composition and function of the intestinal microbiome (dysbiosis) and obesity, impaired glycemic control, and, consequently, the pathophysiology of type 2 diabetes. These induced epigenetic modifications are regulated by metabolites produced by the gut microbiota, such as short-chain fatty acids (acetate, propionate, butyrate), cysteine, mercaptans, which can influence epigenetic processes through their effects on DNA methylation, acetylation and histone modification. Moreover, the direct effects of the microbial environment on the secretion of incretins by intestinal enteroendocrine cells play an important role. The review discusses some of the mechanisms of epigenetic modifications through which the microbiota influences the development of obesity and type 2 diabetes mellitus.