Bacillus polyfermenticus KJS-2 (BP-KJS-2) was used to produce a lipopeptide-type surfactin. To accomplish this, a surfactin-producing BP-KJS-2 was fermented by soybeans. The surfactin was then purified by a procedure including ethanol treatment and preparative chromatography. Next, the biochemical structure of the purified surfactin was analyzed by electrospray ionization mass spectrometry (ESI-MS) and high-resolution ESI Q-Tof mass spectrometry (QTof MS). In addition, the masses of the four peaks were determined to be 1007, 1021, 1035, and 1049 m/z revealing that the compound was mixture with quasi-molecular ions. Taken together, these findings indicated that the lipopeptide had a cyclic structure and amino acid composition of Gln-Leu-Leu-Leu-Val-Asp-Leu-Leu, and that the major lipopeptide product of BP-KJS-2 is the surfactin isoform. In addition, this lipopeptide showed strong antimicrobial activity against bacteria at the level of 0.05 mg/mL.