Currently, there is no available tool to exactly identify and quantify all 48 Pseudo-nitzschia species at once. In this study, we applied massively parallel sequencing-based technology to investigate the distribution and population dynamics of this genera in Tokyo Bay. We also attempted to quantify abundances of each species using both the relative abundance detected in the massively parallel sequencing-based survey and the cell count data obtained by light microscopic observation. Pseudo-nitzschia species appeared constantly in the sampling location from July 10 - September 9, 2016. The cell densities fluctuated from 2 to 300 cells mL-1 (n = 10). Fourteen operational taxonomic units (OTUs) of Pseudo-nitzschia were detected, and 99.9% of the massively parallel sequencing (MPSs) were this genus. The most dominant OTUs each contained a single species by abundance, these were P. multistriata, P. pungens, P. fraudilenta, P. multiseries, and P. galaxiae, in that order. Species identification was possible in 10 of the 14 OTUs. The cell abundances of the top five species were estimated at 1,976-246,395, < 0.03-52,999, 5-42,820, 4-24,617, and < 0.03-1,007 cells L-1, respectively. The detection limit was 0.03 cells L-1.