BACKGROUND Myxococcus xanthus is a gram-negative bacterium that undergoes spectacular development to form multicellular fruiting bodies under nutrient deprivation. Inside a fruiting body, vegetative cells differentiate into spores. A number of sigma factors have been shown to play roles in the regulation of gene expression in the M. xanthus life cycle. Additional sigma factors were searched to further explore the M. xanthus life cycle. RESULTS A new sigma factor was identified, SigD, which consists of 297 amino acid residues. Two transcription initiation sites for the sigD gene were detected by primer extension analysis using total RNA from the vegetative and developmental cells, one of which was specific for development. The characterization of sigD-lacZ fusion strains demonstrated that sigD expression increased during entry into stationary phase of vegetative growth and during early development. A deletion mutant of sigD exhibited growth defects during the late-log phase and stationary phase, with dramatically reduced cell viability. The patterns of protein synthesis at late log phase of vegetative growth and at early development on CF agar plates were significantly different between the deletion mutant and the wild-type strain. The deletion mutant was more sensitive to various stresses when compared with the wild-type strain and did not accumulate trehalose in response to osmotic stress. The deletion mutant also showed a significant delay in fruiting body formation and sporulation and yielded fewer spores than the wild-type strain. CONCLUSIONS SigD shows characteristic features of the stationary phase sigma factors and also plays important roles in multicellular differentiation of M. xanthus.