The establishment of compartment-specific transcription in sporulating cells of B. subtilis is governed at the level of the activity of transcription factor sigma(F). Genetic experiments have suggested that SpollAA and SpollAB, the other products of the sigma(F) operon, are involved in regulating sigma(F) activity. This activity is inhibited in the predivisional cell but specifically released from inhibition in the prespore about 1.5 hr after sporulation is induced. We now show that purified SpollAB inhibits transcription directed by sigma(F) in vitro. We note that the amino acid sequence of SpollAB shows some similarity to a group of bacterial histidine protein kinases, and we find that SpollAB is indeed a protein kinase that phosphorylates SpollAA on a serine residue. We suggest that this phosphorylation is responsible for the compartment-specific release of sigma(F) activity, perhaps through the formation of a tight complex between SpollAB and phosphorylated SpollAA.