Mesozooplankton have been known to be important consumers of phytoplankton, and the community plays an important role in removing the primary production in the marine ecosystem. In the present study, mesozooplankton grazing on phytoplankton were studied in situ at two sampling stations (TM4 and TM8) in Tolo Harbour. HPLC analysis showed that diatoms were the dominant phytoplankton in the two stations throughout the year, and contributed on average to over 40% of total phytoplankton biomass. Dinoflagellates were the second most abundant group of phytoplankton in the two monitoring stations, while the contribution of haptophytes, green algae, cyanobacteria, and cryptophytes was negligible. Feeding experiments, combined with HPLC pigment analysis, were conducted to measure mesozooplankton selective feeding on phytoplankton. The results demonstrated that mesozooplankton displayed a clear feeding selectivity for phytoplankton in Tolo Harbour. Firstly, mesozooplankton showed strong preference for the phytoplankton with the size of 20–200 μm, which suggested that the grazing selectivity and grazing rates of mesozooplankton were affected by the size of the food particles. On the other hand, mesozooplankton assemblages in Tolo Harbour displayed significant feeding selectivity for diatoms, dinoflagellates, and cryptophytes over other types of phytoplankton. The three algae groups are all the major phototrophic components in marine planktonic communities, and they often cause red tides in the marine environment. These results, taken together, suggested that mesozooplankton should play an important role in the regulation of red tides.