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σD is an alternative σ factor that possesses a core-independent promoter −10 element binding specificity despite the lack of a distinct footprint on its cognate promoter. We wished to determine whether this property is common to alternative σ factors. To this end, we over-expressed B. subtilis σB in Escherichia coli and analyzed its DNA binding ability by electrophoretic mobility shift assay and DNase I footprinting. The major complex formed by σB and its cognate promoter DNA is heparin-sensitive. However, in contrast to the −10 element binding specificity observed for B. subtilis σD, the promoter binding of σB is specific for the −35 element. These and other results clearly demonstrate that alternative σ factors possess different promoter-binding characteristics, and make core-independent contributions to recognition of their cognate promoters.The Bacillus subtilis σB specifically binds to its cognate promoter as analyzed by electrophoretic mobility shift assay and DNase I footprinting. The σB-promoter binding is specific for -35 element which is different from the -10 specificity observed for σD. Thus, the alternative σ factors possess different promoter-binding characteristics and make core-independent contributions to recognition of their cognate promoters.