The purpose of this study is to develop a fermentation process for production of functional fermented foods from domestic black soybean by Rhizopus spp. The functional components of fermented black soybean and its physiological function will also be investigated. These results can provide information for establishment of a fermentation process for production of functional fermented black soybean. A fast, precise method is presented for the efficient separation of four isoflavones by high performance liquid chromatorgraphy. The content of isoflavones and 1,1-diphenyl-2-dipicrylhydrazyl (DPPH) radical scavenging test reached to the best by extracted at 65℃ for 2 h. Studies on solid state fermentation by tempeh-like process and the changes of metabolites in black soybeans Tainan NO.3 were investigated by using Rhizopus spp. It was found that the conversion of isoflavones glycosides (daidzin ; genistin) in black soybean to isoflavones aglycones (daidzein ; genistein) was contributed to β-glucosidase activity in fermented black soybeans produced by Rhizopus spp. According to the content of isoflavones aglycones formation, scavenging effect and cultivation time, fermented dehulled black soybeans with R. oligosporus NTU-5 was selected to further isolation and purification of antioxidant. A fraction 3 had the highest scavenging effect was isolated from silica gel column chromatography, eluting with ethyl acetate/n-hexane (1/2, v/v). Then, the fraction 3 was analyzed and purified by TLC and semi-preparative HPLC. Daidzein, genistein and an unknown antioxidative compound SSFE-PA were isolated. The recovery of daidzein and genistein were 94.6% and 58.6%, respectively. The IC50 value of SSFE-PA for DPPH free radicals was 9.8 μg/mL. The molecular weight of SSFE-PA was 287 dalton analyzed by LC/MS. A submerged fermentation of black soybean Tainan NO.3 was also investigated by R. oligosporus NTU-5. It was found that the isoflavones glycosides in black soybean Tainan NO.3 was converted to isoflavones aglycones via the submerged fermentation of R. oligosporus NTU-5.