Bacillus subtilis JA produces a broad spectrum of bioactive lipopeptides with great potential applications in agriculture and industry. Crude lipopeptides were extracted with 100% methanol from the precipitate which was obtained by adding 6 mol/L HCl to the cell-free culture broth. The crude extract was separated on a Diamonsil C18 column (5 microm, 250 mm x 4.6 mm) in reversed-phase high performance liquid chromatography (HPLC) system to separate the lipopeptide homologues. Five peaks were eluted from HPLC. Electrospray ionization mass spectrometry (ESI-MS) was used to analyze each HPLC fraction. The results showed three series of ion peaks. According to the values of m/z, the three series of ions were classified into surfactin, iturin and fengycin homologues, which were well-known biosurfactants produced by B. subtilis strains. The major ions were structurally characterized using tandem mass spectrometry. This study suggested a reasonable method for the isolation and identification of lipopeptides produced by B. subtilis strains.