In this study, we monitored the temporal variation of community diversity of plankton species in Osaka Bay, which is facing a serious problem of harmful algal blooms (HABs). We used the weekly monitored data of plankton assemblages collected using massively parallel sequencing (MPS)-based technique in Osaka Bay from February to May during 2012-2014.Our result showed that the community diversity of plankton assemblage in Osaka Bay decreased sharply at the beginning of March in 2013 and 2014. Whereas such decline did not happened in 2012. On the other hand, the bloom of A. tamarense in 2013 and 2014 stated at the beginning of April. The results of temporal variation of community structure showed that the decline of community diversity of plankton assemblage may trigger the initiation of the bloom of Alexandrium tamarense, causing mass outbreak of paralytic shellfish poisoning in Osaka Bay by penetrating shallow/open space and acquiring their niche.