Listeria monocytogenes has the ability to regulate and fine tune gene expression to adapt to diverse stress conditions encountered during foodborne transmission. To further understand the specific contributions of alternative Sigma factors to regulation of L. monocytogenes gene expression, deep RNA sequencing was performed on L. monocytogenes strain 10403S and five isogenic mutants (four strains bearing in-frame null mutations in three out of four alternative Sigma factor genes, ΔCHL, ΔBHL, ΔBCL and ΔBCH and one strain bearing null mutations in all four genes, ΔBCHL), grown to stationary phase. Our data showed that 184, 35, 34, and 20 genes were positively regulated by SigmaB, SigmaL, SigmaH, and SigmaC (posterior probability > 0.9 and fold change [FC] > 5.0), including 112 and 6 genes identified as directly regulated by SigmaB and SigmaH, respectively (as supported by identification of appropriate putative upstream promoter elements). SigmaB-dependent genes showed the highest FC (based on comparisons between the ΔCHL and the ΔBCHL strain) with 44 genes showing a FC > 100; only four SigmaL-dependent, and no SigmaH- or SigmaC-dependent genes showed FC >100. SigmaB also directly up-regulated four ncRNAs as well as two long 5’ untranslated regions (UTRs) that overlapped other transcription units in the opposite strand; we did not identify noncoding RNA features directly regulated by other alternative Sigma factors. While SigmaB-regulated genes identified in this study are involved in a diversity of pathways and functions, SigmaL appears to largely regulate genes involved in a few specific metabolic pathways, including positive regulation of a number of operons encoding phosphoenolpyruvate (PEP)-dependent phosphotransferase systems (PTSs). Overall, our data show that (i) SigmaB and SigmaL directly and indirectly regulate genes involved in a number of energy metabolism-related functions, (ii) alternative Sigma factors are involved in complex regulatory networks and appear to have epistatic effects in stationary phase cells, and (iii) SigmaB regulates multiple stress response pathways while SigmaL and SigmaH positively regulate a smaller number of specific pathways.