To examine both direct and indirect effects of macrozooplankton on phytoplankton species in Lake Biwa, we conducted in situ grazer-gradient experiments under different nutrient levels in summer, when Daphnia galeata dominated, and in autumn, when Eodiaptomus japonicus dominated. The experiments revealed that grazing pressure on phytoplankton was highly dependent on zooplankton species composition. Smaller phytoplankton species such as Stephanodiscus carconensis were more grazed when D. galeata was abundant, whereas large colonial diatom species such as Aulacoseira granulata were preferentially grazed when E. japonicus dominated. In addition, indirect effect of macrozooplankton through nutrient regeneration was suggested, although the magnitude of nutrient regeneration effects seemed to differ between D. galeata and E. japonicus. Specifically, growth rates of Sphaerocystis schroeteri were stimulated more by E. japonicus than by D. galeata. Macrozooplankton also enhanced the growth rates of colonial cyanobacteria such as Microcystis incerta, probably through decreasing the density of microzooplankton grazers (ciliates and rotifers). The results suggest that the effects of large zooplankton on phytoplankton populations are species-specific and cannot be understood without consideration of changes in abundance of other components of plankton communities. [KEYWORDS: Grazing - Lake Biwa - Nutrient regeneration - Species-specific response] ; To examine both direct and indirect effects of macrozooplankton on phytoplankton species in Lake Biwa, we conducted in situ grazer-gradient experiments under different nutrient levels in summer, when Daphnia galeata dominated, and in autumn, when Eodiaptomus japonicus dominated. The experiments revealed that grazing pressure on phytoplankton was highly dependent on zooplankton species composition. Smaller phytoplankton species such as Stephanodiscus carconensis were more grazed when D. galeata was abundant, whereas large colonial diatom species such as Aulacoseira granulata were preferentially grazed when E. japonicus dominated. In addition, indirect effect of macrozooplankton through nutrient regeneration was suggested, although the magnitude of nutrient regeneration effects seemed to differ between D. galeata and E. japonicus. Specifically, growth rates of Sphaerocystis schroeteri were stimulated more by E. japonicus than by D. galeata. Macrozooplankton also enhanced the growth rates of colonial cyanobacteria such as Microcystis incerta, probably through decreasing the density of microzooplankton grazers (ciliates and rotifers). The results suggest that the effects of large zooplankton on phytoplankton populations are species-specific and cannot be understood without consideration of changes in abundance of other components of plankton communities. [KEYWORDS: Grazing - Lake Biwa - Nutrient regeneration - Species-specific response]