To elucidate the trophic link between classical and microbial food webs in the coastal ecosystem of Matsu Island during the warmer (27.5°C) and colder (16°C) months, we estimated the impact of mesozooplankton and microzooplankton grazing on > 20 μm and < 20 μm phytoplankton groups, respectively. In the warmer months, the > 20 μm fraction of Chl a accounted for more than 70% of the total Chl a; however, the Chl a > 20 μm fraction contributed little to the total phytoplankton biomass, at about 16%, in the colder months. Overall, the < 20 μm fraction represented 26 and 90% of the < 200 μm daily primary production in the warmer and colder months, respectively. Furthermore, the grazing loss of mesozooplankton on microzooplankton was 4.7 mgC m-3 d-1 in the warmer months; however, no significant loss rate was measured in the colder months. The results showed that large autotrophs (> 20 μm) were available for direct mesozooplankton ingestion, which indicated that they could be considered as an important link in the complex food web structures, particularly during the warmer season.