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<i>Bacillus subtilis</i> is an ideal host for secretion and expression of foreign proteins. The promoter is one of the most important elements to facilitate the high-level production of recombinant protein. To expand the repertoire of strong promoters for biotechnological applications in <i>Bacillus</i> species, 14 highly transcribed genes based on transcriptome profiling of <i>B. pumilus</i> BA06 were selected and evaluated for their promoter strength in <i>B. subtilis</i>. Consequently, a strong promoter P₂₀₆₉ was obtained, which could drive the genes encoding alkaline protease (<i>aprE</i>) and green fluorescent protein (GFP) to express more efficiency by an increase of 3.65-fold and 18.40-fold in comparison with the control promoter (P_aprE), respectively. Further, promoter engineering was applied to P₂₀₆₉, leading to a mutation promoter (P_2069M) that could increase GFP expression by 3.67-fold over the wild-type promoter (P₂₀₆₉). Moreover, the IPTG-inducible expression systems were constructed using the <i>lac</i> operon based on the strong promoters of P₂₀₆₉ and P_2069M, which could work well both in <i>B. subtilis</i> and <i>B. pumilus</i>. In this study, highly efficient expression system for <i>Bacillus</i> was constructed based on transcriptome data and promoter engineering, which provide not only a new option for recombinant expression in <i>B. subtilis</i>, but also novel genetic tool for <i>B. pumilus</i>.