Kawaguchipeptin B, an antibacterial cyclic undecapeptide, was isolated from the cultured cyanobacterium Microcystis aeruginosa (NIES-88). Its structure was elucidated as 1 on the basis of 2D NMR data and chemical degradation. Kawaguchipeptin B (1) inhibited the growth of the Gram-positive bacterium Staphylococcus aureus at a concentration of 1 microgram/mL (MIC).