Temporal and compartment-specific control of gene expression during sporulation in Bacillus subtilis is governed by a cascade of four RNA polymerase subunits. sigmaF in the prespore and sigmaE in the mother cell control early stages of development, and are replaced at later stages by sigmaG and sigmaK, respectively. Ultimately, a comprehensive description of the molecular mechanisms underlying spore morphogenesis requires the knowledge of all the intervening genes and their assignment to specific regulons. Here, in an extension of earlier work, DNA macroarrays have been used, and members of the four compartment-specific sporulation regulons have been identified. Genes were identified and grouped based on: i) their temporal expression profile and ii) the use of mutants for each of the four sigma factors and a bofA allele, which allows sigmaK activation in the absence of sigmaG. As a further test, artificial production of active alleles of the sigma factors in non-sporulating cells was employed. A total of 439 genes were found, including previously characterized genes whose transcription is induced during sporulation: 55 in the sigmaF regulon, 154 sigmaE-governed genes, 113 sigmaG-dependent genes, and 132 genes under sigmaK control. The results strengthen the view that the activities of sigmaF, sigmaE, sigmaG and sigmaK are largely compartmentalized, both temporally as well as spatially, and that the major vegetative sigma factor (sigmaA) is active throughout sporulation. The results provide a dynamic picture of the changes in the overall pattern of gene expression in the two compartments of the sporulating cell, and offer insight into the roles of the prespore and the mother cell at different times of spore morphogenesis.