On the basis of measuring the DNA damage by quantitative PCR, we developed an experimental system for observation of DNA damage and its repair process in the fission yeast mitochondria. Using this method, we studied the repair capacity of UV-damaged mitochondrial DNA (mtDNA) in various DNA repair mutants. UV endonuclease (Uve1p) is known to participate in repair of UV damage DNA in both nucleus and mitochondria of the yeast. In this study, we found that Uve1p strongly involves in restoration of damaged mtDNA within 2 hours after UV-irradiation. Flap en- donuclease (Rad2p) is known to act on the repair pathway initiated by Uve1p in nucleus, whereas Rad2p-deficient mutant could repair mtDNA at the same rate as the wild type. Unknown enzyme that alternates with Rad2p is necessary to complete the Uve1p pathway in mitochondria. In Uve1p- deficeint mutant (uve1∆) most of the mtDNA damages disappeared by extending repair time to 8 hours. We tested the involvement of the autophagy in the late repair reaction, but an Atg1-lacking mutant could restored mtDNA damage. Copy numbers of mtDNA in the uve1∆ cells increased to 2.5-fold during 8 hours of repair time, and the extension of the cell length was observed. These results suggest the possibility that newly synthesis of mtDNA in mitochondria caused an apparent repair of mtDNA in late repair time.