This study investigated the potential health benefits of two different species of black legume [ Glycine soja Sieb. et Zucc. and Glycine max (L.) Merr.] on diet-induced obesity. C57BL/6 mice were fed a high-fat diet (HFD) supplemented with 20% (w/w) black legume for 12 weeks, and the effects on weight gain, serum lipid levels, liver histology, gut fermentation, and microbiome profile were examined. Consumption of black legumes improved the blood lipid profile and increased fecal propionate and butyrate contents; this was accompanied by a reduction in hepatic steatosis and adipocyte size. High-throughput pyrosequencing of 16S rRNA revealed that black legumes prevented the loss of fecal microbiota diversity and richness caused by a HFD and decreased the relative abundance of Verrucomicrobia while increasing that of Bacteroidetes. Collectively, dietary supplementation with black legumes was found to have attenuated many of the adverse health consequences associated with a HFD and modulated gut microbiota in a positive way.