The alternative sigma factor sigma(B) contributes to transcription of stress response and virulence genes in diverse gram-positive bacterial species. The composition and functions of the Listeria monocytogenes and Listeria innocua sigma(B) regulons were hypothesized to differ due to virulence differences between these closely related species. Transcript levels in stationary-phase cells and in cells exposed to salt stress were characterized by microarray analyses for both species. In L. monocytogenes, 168 genes were positively regulated by sigma(B); 145 of these genes were preceded by a putative sigma(B) consensus promoter. In L. innocua, 64 genes were positively regulated by sigma(B). sigma(B) contributed to acid stress survival in log-phase cells for both species but to survival in stationary-phase cells only for L. monocytogenes. In summary, (i) the L. monocytogenes sigma(B) regulon includes >140 genes that are both directly and positively regulated by sigma(B), including genes encoding proteins with importance in stress response, virulence, transcriptional regulation, carbohydrate metabolism, and transport; (ii) a number of L. monocytogenes genes encoding flagellar proteins show higher transcript levels in the Delta sigB mutant, and both L. monocytogenes and L. innocua Delta sigB null mutants have increased motility compared to the respective isogenic parent strains, suggesting that sigma(B) affects motility and chemotaxis; and (iii) although L. monocytogenes and L. innocua differ in sigma(B)-dependent acid stress resistance and have species-specific sigma(B)-dependent genes, the L. monocytogenes and L. innocua sigma(B) regulons show considerable conservation, with a common set of at least 49 genes that are sigma(B) dependent in both species.