We found that the three genotypes of the FOXC2 gene were differentially associated with the intestinal microbiota, with the abundance of Coriobacteriia, Clostridiales, Clostridiaceae, and Collinsella in the gut microbes of patients with CC-type T2DM being significantly higher than that of patients with TT-type T2DM. The gene discussed is FOXC2; the disease is type 2 diabetes mellitus.