Harmful algal blooms (HABs), such as dinoflagellate blooms, have adverse effects on coastal water environments, causing seafood contamination and aquaculture economic losses. Based on historical HAB records data (1983–2017) and phytoplankton data (1982–2008), field investigation and laboratory experiments on frequently bloomed dinoflagellate species, we analyzed the possible mechanisms of high frequency dinoflagellate blooms in Daya Bay, South China Sea. The HAB records data show that the proportion of dinoflagellate blooms increased from 15％ before 1994 to 77.27％ after 2011. The bloom occurred mostly in summer (57.58％) in Yaling Bay (76.92％). The species inducing dinoflagellate blooms tended to be singular over time, with high proportion of Scrippsiella trochoidea (42.86％–88.88％). Laboratory experiment and field investigation of S . trochoidea bloom showed that this species grew rapidly at 30 ℃ and 32.1 ℃ ( r =0.47, P 7 m/s), which disturbed the resting cysts in the sediment and bring them into surface layer. Taking into account of environmental parameters, algae source, and atmospheric conditions, the probable mechanism of S . trochoidea bloom could be explained. The cysts were resuspended by the spring tide or strong wind, germinated at the bottom layer, reproduced rapidly at higher temperature, and then aggregated in the inner bay (Yaling Bay), resulting the frequent S . trochoidea bloom. Considering the influences of global warming and human activities, it should be taken more attention that dinoflagellate blooms might increase along the coastal waters.