Cyanobacterin is a secondary metabolite produced by the cyanobacterium, Scytonema hofmanni. Highly purified cyanobacterin was found to inhibit the growth of many cyanobacteria at a minimum effective dose of 2 μg/ml (4.6 μM). The antibiotic had no effect on eubacteria including the photosynthetic Rhodospirillum rubrum. The site of action of cyanobacterin was further investigated in the unicellular cyanobacterium, Synechococcus sp. Electron micrographs of antibiotic-treated Synechococcus cells indicated that cyanobacterin affects thylakoid membrane structure. The antibiotic also inhibited light-dependent oxygen evolution in Synechococcus cells and in spheroplasts. These data support our conclusion that cyanobacterin specifically inhibits photosynthetic electron transport. This activity is similar to herbicides such as 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU). The anhydro analog of cyanobacterin had no biological activity.