Aims Gut microbiota dysbiosis is known to be associated with diabetes, however the findings of previous studies are conflicting. To clarify the association between type 2 diabetes and the gut microbiota, the present study analyzed the composition of fecal gut microbiota and its correlation with specific clinical parameters in newly-diagnosed, treatment-naive diabetic patients and healthy controls. Methods A total of 50 patients with newly diagnosed type 2 diabetes and 50 healthy control subjects were enrolled in the study. Fecal samples, blood samples and food diaries were collected from the diabetic patients prior to, and 3-months after the start of their anti-diabetic treatment. These samples were also collected from the healthy controls. The gut microbiota was characterized by 16S rRNA analysis using quantitative polymerase chain reaction. Results The fecal count of Lactobacillus was significantly higher, while Clostridium coccoides and Clostridium leptum were significantly lower in the diabetic patients compared with the healthy controls. Lactobacillus was significantly positively correlated with glucose, glycated hemoglobin, and the homeostatic model assessment, whereas C. coccoides and C. leptum were significantly negatively correlated with the diabetic parameters. In addition, the newly-diagnosed diabetic patients had a significant decrease in the presence of C. coccoides and C. leptum after 3 months of treatment compared with before treatment. Conclusions The amount of fecal Lactobacillus, C. coccoides and C. leptum was significantly different between the patients with type 2 diabetes and the healthy controls. The levels of Clostridium were also significantly changed after 3-months of treatment in the diabetic patients. Further research is needed to clarify the correlation or causal relationship between the gut microbiota dysbiosis and type 2 diabetes.