Today, metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUO) are distinguished. Adipose and muscle tissues can determine the obese phenotype due to adipokine and myokine production. Gut microbial community is also involved in MHO. The study was aimed to reveal the features of adipokine and myokine levels and their association with the gut microbiome alpha diversity in patients with MHO and MUO. A total of 265 subjects were divided into two groups: healthy individuals and obese patients. The latter were divided into two subgroups: patients with MHO and patients with MUO. Body mass index, waist circumference, HOMA-IR, adipokine and myokine levels, gut microbiome taxonomic composition, alpha diversity indices were defined in all the surveyed individuals, lipid and carbohydrate metabolism was also assessed. Significant differences in the adipokine and myokine levels and their association with the gut microbiome diversity indicators were revealed in patients with different obese phenotypes. Patients with MHO and MUO showed significantly lower adiponectin levels (р < 0.05) and significantly higher leptin and asprosin levels (р < 0.05) than healthy individuals. Patients with MUO had lower adiponectin and leptin levels (p < 0.05) than patients with MHO. Significantly higher FGF21 levels were observed in patients with MUO. Large-scale correlation analysis revealed the relationship between the glucose levels and the gut microbiome diversity indices that was missing in patients with MUO. This indicated the loss of the microbiota diversity effects on the blood glucose control in individuals with MUO, as well as different regulatory roles in the gut microbiome‒liver‒muscle/adipose tissue axes of individuals with MHO and MUO played by gut microbiota. The findings show the relationship between the gut microbiome diversity and the obese phenotype.