Bacillus subtilis GlcP regulates a secondary metabolism, the neotrehalosadiamine synthesis pathway, by repressing a neotrehalosadiamine biosynthesis operon in response to glucose present in the medium. Here, we investigated, by use of transcriptome, additional effects of glcP disruption on other gene expression. In the GlcP-null mutant, the expression of alsSD and maeN was decreased, while the expression of licBCAH, ntdABC, yyaH-maa, and yyaJ was increased. The effect caused by loss of GlcP function was, however, completely negated in a mutant lacking the ability to synthesize neotrehalosadiamine. Moreover, addition of neotrehalosadiamine into the growth medium had no effect on the expression of these genes, indicating that GlcP-promoted regulation was exerted depending on de novo neotrehalosadiamine synthesis rather than neotrehalosadiamine per se. These findings suggest that GlcP participates in regulation of certain genes by repressing the neotrehalosadiamine biosynthesis operon. This novel regulation system may provide new insights into study of B. subtilis gene expression.