Soluble extracts of the cyanobacterium Anabaena variabilis ATCC 29413 and an engineered mutant that lacks an intracellular protease cleaving after Lys and Arg (Maldener, Lockau, Cai, and Wolk, Mol. Gen. Genet. 225, 113-120 (1991)) were separated by ion exchange chromatography, and protease profiles determined using azocasein, Nα-benzoyl-ᴅ,ʟ arginine- 4-nitroanilide and N-carbobenzoxy-glycyl-ʟ-proline-4-nitroanilide as substrates. A second enzyme cleaving at the carboxyl side of lysine and arginine, and a prolyl endopeptidase were detected, enriched and characterized. Both proteolytic enzymes appear to be located in the periplasm.