The small bitopic division protein FtsL is an essential part of the division machinery (divisome) in most eubacteria. In Bacillus subtilis FtsL is a highly unstable protein and the turnover has been implicated in regulation of division in response to DNA damage. N-terminal deletions and a domain swap experiment identified the short cytoplasmic domain of FtsL as being required for instability. We then identified a zinc metalloprotease, YluC, required for turnover, and likely sequence motifs involved in substrate recognition. YluC belongs to the site-2-protease (S2P) family of proteases involved in regulated intramembrane proteolysis (RIP), which plays a role in diverse regulatory phenomena from bacteria to man. The yluC mutant, and strains with N-terminal truncations of ftsL have a short cell phenotype, indicating that that FtsL is normally rate-limiting for division. Coexpression experiments of FtsL and YluC in Escherichia coli corroborated a model in which FtsL is directly cleaved by the membrane metalloprotease. The results shed new light on the regulation of cell division in B. subtilis and identify a novel class of targets for RIP.