Next-generation sequencing (NGS) technologies have made it possible to obtain millions of sequence reads in a single experiment, and massively parallel sequencing (MPS) is currently revolutionizing survey of environmental DNA (eDNA), because this technology enables us to detect several hundreds of operational taxonomic units (OTUs) of bacteria and eukaryotes from aquatic environmental samples and facilitates the detection of low-abundance populations from complex communities. The significant advantage of applying metabarcoding technology for monitoring biodiversity is the great potential for more precise species identification based on genetic information, especially species that are indistinguishable by the conventional morphology-based microscopic observation. In the recent 10 years, we have had research projects to evaluate eukaryotic biodiversity utilizing metabarcoding techniques among different marine ecosystems, i.e. sea ice, aquaculture and fish grounds, coral reef, macroalgal seedbed ecosystems from the northernmost to the southernmost area of Japan (from coastal waters to offshore and deep sea). We have collected >5,000 eDNA samples and accumulated the information on bacteria, fungi, microalgae, protists, zooplankton distribution and appearances. We believe that this study can enhance our comprehensive understanding of primary productivity and marine micro food webs.