We compared the production of poly-γ-glutamate (γ-PGA), protease and amylase, the phage type, and inheritance of the insertion sequence (IS) IS4Bsu1among 90 Bacillus subtilis strains isolated from fermented soybean foods from Southeast to East Asia with those of a B. subtilis (natto) starter strain. All the isolates produced high levels of protease but various levels of amylase. None of them belonged to the standard phage type of B. subtilis, but 11 strains appeared to belong to the same phage type as B. subtilis (natto). Sixty-three isolates produced γ-PGA, while 28 isolates carried the IS element, the copy number of which ranged from 1 to 17. The IS appeared to be widely distributed among B. subtilis strains from non-salted types of fermented soybeans, such as “Tua Nao” of Thailand (90%) and “Kinema” of Nepal (56%), while a relatively small fraction (15%) of B. subtilis strains from salted types of fermented soybeans, e.g. Chinese “Douchi”, harbored the IS. No relationship was apparent between the IS element and γ-PGA production. Nucleotide sequencing demonstrated that the IS elements of the randomly selected 9 isolates had a sequence identical with that of B. subtilis (natto) and those of another 4 strains showed only one to three mutations. These results together imply that IS4Bsu1 was recently distributed among B. subtilis strains that predominantly occur in cooked soybeans.