|In the current dam reservoirs and natural lakes, there are growing concerns about increasing occurrence of abnormal algae proliferation due to climate change. The abnormal algae proliferation causes algal bloom, musty odor, freshwater red tide and other different problems in drinking water supply. In this study, a novel monitoring method of planktons in dam reservoirs and natural lakes was developed, which is focused on 16S and 18S rRNA gene sequences using a next generation sequencer (NGS). This investigation with an NGS detected a remarkably higher number of species compared to the conventional microscopic examination method: 726 bacterial species and 522 planktonic species using an NGS, and 1 bacterial species and 24 planktonic species using a microscopy. All species identified by microscopy were detected by NGS, except for Trachelomonas sp., which was not detected for some reasons. This DNA-based method was presumed to detect species at low concentration which could not be detected by microscopy. Therefore, the effectiveness of this DNA-based method using an NGS was suggested to maintain and control the water quality of dam reservoirs and lakes.