We determined bacterial migration into doenjang from its components, meju and solar salt using culture-based and 16S rRNA gene-based culture-independent techniques (pyrosequencing of total DNA). Pyrosequencing results suggested that the bacterial communities of meju, but not solar salt, significantly affected those of doenjang communities. Culture-based pyrosequencing analysis yielded similar results. These results indicate that most predominant bacterial species in doenjang migrated from meju, not solar salt. We therefore believe that the present study is one of the most comprehensive comparisons of bacterial communities of fermented soybeans using culture-dependent and -independent methods. Furthermore, pyrosequencing of the V3 and V4 regions of bacterial 16S rRNA did not distinguish among Bacillus amyloliquefaciens, B. siamensis, and B. velezensis as well as between Enterococcus faecium and E. hirae.