In copepods, morphologically-indistinguishable but genetically-different cryptic species complexes are frequently found, such as the Acanthodiaptomus pacificus complex that is commonly found in Japanese lakes and ponds. In the present study, the fauna of Japanese freshwater calanoid copepods were extensively reexamined using molecular techniques, and the autecology of each calanoid species was deduced based on the molecular identifications. Specimens were collected throughout Japan, identified by their morphological diagnostic characteristics, and then sequenced for the mitochondrial cytochrome c oxidase subunit 1 (mtCOI). In total, 13 species were found in the present study, and in most cases, only one species was collected from each waterbody. The A. pacificus complex occurred not only in high mountain lakes and pools of mountain moors but also in water bodies on low-altitude plains. The occurrence of the other species was restricted to low-altitude waterbodies, which were mostly man-made irrigation ponds. Heliodiaptomus nipponicus and Neutrodiaptomus formosus, which are endemic to Japan, were found only in irrigation ponds, indicating that artificial waterbodies are currently indispensable to maintain the diversity of Japanese freshwater zooplankton. The results of mtCOI sequencing revealed the existence of putative cryptic species complexes such as Neutrodiaptomus formosus in Japan, and Neodiaptomus schmackeri, Sinodiaptomus sarsi, Heliodiaptomus kikuchii, and Eurytemora affinis across their Asian range. It is thus strongly recommended that any outcome of the freshwater zooplankton monitoring programs always be supplemented with DNA sequences in order to render that outcome sound and reliable also for future studies.