Dilution experiments were conducted to investigate microzooplankton grazing impact on phytoplankton of different taxonomic groups and size fractions (<5, 5–20, 20–200μm) during spring and summer bloom periods at two different sites (inner Tolo Harbour and Tolo Channel) in the Tolo Harbour area, the northeastern coastal area of Hong Kong. Experiments combined with HPLC pigment analysis in three phytoplankton size fractions measured pigment and size specific phytoplankton growth rates and microzooplankton grazing rates. Pigment-specific phytoplankton growth rates ranged between 0.08 and 3.53d−1, while specific grazing rates of microzooplankton ranged between 0.07 and 2.82d−1. Highest specific rates of phytoplankton growth and microzooplankton grazing were both measured in fucoxanthin in 5–20μm size fraction in inner Tolo Harbour in summer, which coincided with the occurrence of diatom bloom. Results showed significant correlations between phytoplankton growth and microzooplankton grazing rates. Microzooplankton placed high grazing pressure on phytoplankton community. High microzooplankton grazing impact on alloxanthin (2.63–5.13) suggested strong selection toward cryptophytes. Our results provided no evidence for size selective grazing on phytoplankton by microzooplankton. •Microzooplankton placed high grazing pressure on phytoplankton community.•High g/µ ratio for alloxanthin indicated a preference by MZP toward cryptophytes.•Results provided no evidence for selective grazing by MZP on phytoplankton size.