The spoIIE gene is essential for the compartment-specific activation of transcription factor sigma(F) during sporulation in Bacillus subtilis. SpoIIE is a membrane protein that is targeted to the potential sites of asymmetric septation near each pole of the sporulating cell. The cytoplasmic carboxy-terminal domain of SpoIIE contains a serine phosphatase that triggers the release of sigma(F) in the prespore compartment after septation. To understand how septum-located SpoIIE is activated selectively in the prespore, we examined the distribution of a SpoIIE-GFP fusion protein. We show that the polar bands of SpoIIE protein actually form sequentially and that the most prominent band develops at the pole where the prespore forms. We also show that the protein is sequestered to the prespore side of the asymmetric septum. Sequestration of SpoIIE into the prespore compartment provides a mechanism that could explain the cell specificity of sigma(F) activation.