Abstract Background Alternative σ factors are important transcriptional regulators in bacteria. While σB has been shown to control a large regulon and play important roles in stress response and virulence in the pathogen Listeria monocytogenes, the function of σH has not yet been well defined in Listeria, even though σH controls a large regulon in the closely related non-pathogenic Bacillus subtilis. Results Using RNA-seq characterization of a L. monocytogenes strain with deletions of all 4 genes encoding alternative σ factors (ΔBCHL), which was further modified to overexpress sigH (ΔBCHL::P rha -sigH), we identified 6 transcription units (TUs) that are transcribed from σH-dependent promoters. Five of these TUs had not been previously identified. Identification of these promoters was facilitated by use of a bio-informatics approach that compared normalized RNA-seq coverage (NRC), between ΔBCHL::P rha -sigH and a ΔBCHL control, using sliding windows of 51 nt along the whole genome rather than comparing NRC cal...