Underwater shock wave, generated by the imploding detonation of propane-oxygen mixture, was applied for extinction processing of microbes. We filled the water containing microbe into a stainless steel pipe having inner diameter of 10.9 mm, and transmitted the underwater shock waves which have the maximum pressure of about 100MPa. As microbe of the treatment experiments, Microcystis species were used. We found that the mortarity rate of Microcystis species increases gradually with the increase in the number of times of shock processing. Although the maximum mortality rate of Microcystis species was 99.9% in one day after processing, it turned out that it becomes 100% in one week after processing. The mortality rate became small when the value of the consistency of Microcystis species was large.