Aims This study evaluated the effects of a potential probiotic, Bacillus sp., on the growth, serum and hepatic triglyceride, histological features of liver tissues and colonic microflora in high-fat diet-induced obese mice. Methods and Results Sixty male C57BL/6J mice were randomly divided into five groups: mice fed a low-fat diet (Cont), mice fed a high-fat diet (Hf), Hf and orally challenged with Bacillus subtilis (Bs), B. licheniformis (Bl) and a mixture of B. subtilis and B. licheniformis (Bls). Gavage feeding was provided at week 9 and the experiment was continued for 8 weeks. Treatment with B. licheniformis and a mixture of Bacillus sp. attenuated body weight gain at the end of study and enhanced glucose tolerance by sensitizing insulin action in the Hf-fed mice. Lower serum and hepatic triglyceride and epididymal fat weight were observed in Bl and Bls groups than that of Hf group. Lesser hepatic fat deposition was observed in the Bl and Bls groups than in the Hf group. High-throughput sequencing showed that Bacillus sp. supplementation dramatically changed the colonic bacterial community in obese mice. Conclusions Bacillus licheniformis reduced body weight and improved glucose tolerance, obesity and insulin resistance in Hf-fed mice by changing colonic microbiota composition. Significance and Impact of the Study Orally administration of Bacillus licheniformis may reduce body weight and decrease fat deposition by modulating colonic bacterial community in Hf model.