Two bioactive diketopiperazines, cyclo(S-Pro-S-Phe) and cyclo(R-Pro-S-Phe), against Bacillus subtilis (terrestrial), Staphylococcus aureus, and Escherichia coli DH5 were isolated from marine surface sediment bacteria Bacillus subtilis sp.13-2. To our knowledge, this was the first time that cyclo(S-Pro-S-Phe) and cyclo(R-Pro-S-Phe) were isolated from Bacillus subtilis, and the first time that cyclo(R-Pro-S-Phe) was isolated from a natural source. These two compounds were established on the basis of ESI-MS spectral data, as well as NMR 1D and 2D (COSY, HMQC, and HMBC) spectral data.