To study the effects of simulated HAB (Harmful algal blooms) on protozoan community structure, shipboard Prorocentrum donghaiense inoculation experiments (at about 106 cells L-1, equivalent to bloom density) were carried out at stations zzf1, zc18a and ra5 in the East China Sea, a frequent HAB occurrence area, on 27th April, 4th May and 8th May 2005, respectively. The results showed that P. donghaiense at a density of 106 cells L-1 could inhibit the abundance of small-sized aloricate ciliates, but had no significant effect on medium- and large-sized protozoa, which thereby led to a community succession toward medium- or large-sized individuals. Such effects and the degree of impact were closely related to both protozoan and phytoplankton community compositions. At station zzf1, the protozoan community initially dominated by the small-sized aloricate ciliate Cyrtostrombidium sp. changed remarkably and was dominated by the large-sized protozoan Noctiluca scintillans after adding P. donghaiense for 72 h. At station zc18a, the protozoan community initially dominated by medium-sized tintinnid Tintinnopsis beroidea and N. scintillans was still dominated by the two protozoa, and the dominant degree of N. scintillans increased noticeably after adding P. donghaiense for 72 h. At station ra5, the protozoan community initially dominated by the small-sized aloricate ciliate Strombidium sp.2 changed dramatically and was dominated by T. beroidea and the large-sized tintinnid Favella azorica at the end of the experiment. The total abundance of protozoa decreased dramatically at stations zzf1 and ra5 due to the reduction of their dominant species Cyrtostrombidium sp. and Strombidium sp.2, whereas no significant variation was found at station zc18a due to the steady abundance of its dominant species T. beroidea and N. scintillans after adding P. donghaiense for 72 h. The total biomass of protozoa at stations zzf1 and zc18a changed slightly in both control groups and the experimental ones. In contrast, total biomass decreased drastically at station ra5 at the end of the experiments, which might be due to the different phytoplankton composition at the three stations: station zzf1 and zc18a were dominated by non-toxic Scrippsiella trochoidea and Gyrodinium spirale, however station ra5 was dominated by toxic Alexandrium sp.. These results indicate that large scale P. donghaiense HAB could affect protozoan communities and might further exert a profound influence on the structure and function of marine ecosystems.