Hypocrellin B (HB) is a highly effective photosensitizer. One of its derivatives, 5-brominated-hypocrellin B (5-Br-HB) has better photosensitive characterlstics than it. Using Raman spectroscopy, the microcosmic photodamage to DNA sensitized by HB and 5-Br-HB was studied at molecular level. The results showed that when HB and 5-Br-HB were added to the solution of DNA and irradiated, the characteristic Raman frequencies and intensities of DNA changed to various degrees. The photodamage occurred on the whole DNA molecule, including phosphate backbone, deoxyribose and four bases. Not only the conformation but also the configuration of DNA was photodamaged: breakage of some H-bonds, disappearance of B-form conformation, scission of double or single strand and serious damage of four bases. The damage to A-T pairs was stronger than that to C-G pairs and DNA became polynucleotides finally. The 5-Br-HB-photosensitized damage to DNA was stronger than HB, which suggested the better photosensitive characteristics of 5-Br-HB in bioactive environment. The molecular mechanisms of photodamage to DNA sensitized by 5-Br-HB and HB were also elucidated.