The putative physical map of a Bacillus subtilis (natto) strain has been constructed to demonstrate the difference from the strain B. subtilis Marburg. B. subtilis (natto) strains are closely related to the Marburg 168trpC2 strain whose genome was sequenced. Their genome size and organization are also assumed to be similar. The putative SfiI and I-CeuI physical map of a natto strain BEST195 revealed that structure of most genome region is similar to that of 168 but some highly variable chromosome regions are also identified.