Microcystis aeruginosa forms algal bloom in lakes. They produce toxic compounds such as microcystin. Against such algal problems, the effect of UV treatment was examined. In UV treatment, the effect of photoreactivation should be examined. Photoreactivation is a repair mechanism of genomic DNA damage by sunlight irradiation. UV treatment causes DNA damages on target cyanobacteria, however sunlight can repair some of these DNA damages. To examine the effect of photoreactivation, both white and yellow light incubations were employed. White light allows both photoreactivation and photosynthesis, while yellow light prohibits photoreactivation and only allows photosynthesis. Microcystis aeruginosa NIES 98 strain and PCC 7806 strain were used as the test cultures. Those cultures were exposed to low-pressure (LP) or medium-pressure (MP) ultraviolet (UV) lamp, then incubated under white or yellow light. Yellow light incubation method was effective to examine photoreactivation. It was revealed that almost six times UV fluence was required to inactivate 99% of Microcystis aeruginosa, under photoreactivation condition, compared with non-photoreactivation condition. Inhibition of photoreactivation could greatly enhance UV treatment efficiency against Microcystis aeruginosa. One of the practical suggestions is to conduct UV treatment at night, when photoreactivation by sunlight rarely takes place. Highly efficient inactivation was achieved by avoiding photoreactivation.