An immunopotentiating compound has been isolated from the metabolites of Bacillus mycoides under the bioassay-guided isolation and identification for its immunopotentiating effect and chemical structure. The isolation and purification of the compound were consisted of macroporous adsorptive resins, silicagel chromatographic column and Sephadex G-200 chromatographic column. The immunopotentiating effect was assayed in every step isolation. At last, the only substance having the strongest immunopotentiating effect had been isolated and purified. Through the procedure consisiting of Ultra-Violet spectroscopy (UV), IR (Infrared Radiation), Time of Flight Mass Spectrum (TOF-MS), Nuclear Magnetic Resonance (NMR) and Element analysis, the possible structure of compound M had been identified as cyclic (Pro-Gly) dipeptide (C7H10O2N2) (Diketopiperazine). To be determined the immunopotentiating effect, the mice were treated by intraperitoneal injection of cyclic (Pro-Gly) dipeptide in the treatment group and distilled water in the control group. At the 14th day after the injection, the SOD activity and the phagocytosis activities reached the peak value and were significantly higher than those in control group. At the 21st day, the bactericidal activity reached peak value and was significantly higher than that in the control group. From the above results, we concluded that the main active component enhancing the immunity of mice was cyclic (Pro-Gly) dipeptide in the metabolism of Bacillus mycoides.