The effect of hypericin photoactivation on mitochondria of human prostate carcinoma cells was studied using a range of mitochondrial inhibitors. Oligomycin significantly enhanced hypericin phototoxicity while atractyloside and antymicin A conferred a significant protection. Use of myxothiazol did not affect cell survival following hypericin photoactivation. These results signify a protective role for F(1)F(0)-ATP synthase running in reverse mode, and a significant photodamage at the quinone-reducing site of mitochondrial complex III. In light of these results, we performed molecular modeling of hypericin binding to complex III. This revealed three binding sites, two of which coincided with the quinol-oxidizing and quinone-reducing centers. Using submitochondrial particles we examined hypericin as a possible substrate of complex III and compared this to its natural substrate, ubiquinone-10. Our results demonstrate uniquely that hypericin is an efficient substrate for complex III, and this activity is inhibited by myxothiazol and antimycin A. We further demonstrated that hypericin photosensitization completely inactivated complex III with ubiquinone as substrate. The ability to enhance HYP potency by inhibition of F(1)F(0)-ATP synthase or depress HYP efficacy by inhibition at the Qi site of complex III provides a potential to increase the therapeutic index of HYP and amplify its PDT action in tumor cells.