Oxygen-derived free radicals are causative agents of various diseases (e.g., atherosclerosis, inflammation, Parkinson's disease, ischemia-reperfusion injury including cerebral trauma and stroke), and substances with free radical scavenging activities can ameliorate these conditions. In the course of screening for microbial free radical scavengers, we previously isolated benthocyanin A (3) from Streptomyces prunicolor and determined its structure via NMR and X-ray crystallographic experiments. Further investigation led to the isolation of its minor congeners, benthocyanins B (1) and C (2). Herein, we report the structural studies of these metabolites. Isolation was carried out by combined column chromatography, yielding benthocyanin B (1) as dark blue plates and benthocyanin C (2) as violet powder. Their structures were elucidated using physicochemical properties (melting point, UV/visible spectra) and spectroscopic analyses (1H/13C NMR, HMBC, NOE, IR, HRFAB-MS). Benthocyanin B (1) is a regioisomer of 3 with the carboxylic acid group at C-1 instead of C-9. Benthocyanin C (2) contains a phenazine skeleton, a nitrile residue at C-11, and a carboxylic acid group. Both compounds exhibited potent free radical scavenging activities: they inhibited lipid peroxidation in rat microsomes with IC50 values of 0.16 μg/mL (1) and 0.29 μg/mL (2) (30-70 times stronger than vitamin E) and suppressed rat erythrocyte hemolysis with IC50 values of 0.56 μg/mL (1) and 1.30 μg/mL (2).