Abstract: In order to investigate the difference of fermentation strain from different kind of natto,six brands of natto products from three origins were selected,which were Meiwu,Yucheng,Yanjing,Bamboo charcoal,Hokkaido and Benchangshuihu.Fifteen typical colonies of Bacillus subtilis strains with the characteristics of a single colony were isolated from six Natto food produced.They were compared with model strain Bacillus subtilis Natto 1.1086 according to their morphological,physiological,biochemical characters and 16 S rRNA sequence of strain analysis respectively. Results showed that 15 bacterias were Bacillus subtilis strains,in which 10 strains present homology of 99%,3 strains present 98% and 2 present homology 97.5% on 16S rRNA sequence. And the nattokinase of 15 Bacillus natto were measured by method of agarose-fibrin plate. The data indicate both of Nattokinase activity of NB-8 and NB-12 were relatively strong with a result of 1076.663 and 1073.85 U/mL,respectively.