The predation impact of the larvae of pond smelt Hypomesus transpacificus nipponensis on a zooplankton community was studied using mesocosms. The fish significantly depressed the abundances of copepod nauplii and rotifers, especially Hexarthra mira. The vulnerabilities of these prey might be determined by their swimming behavior and population density, suggesting that larval fish selectively prey on zooplankton that have a high encounter rate with the predator. The larvae did not have a negative effect on the densities of cladocerans, but fish predation altered the cladoceran community structure from the dominance of B. longirostris to that of B. fatalis. This result suggests that larval fish predation is an important factor that shifts the species composition of Bosmina in some lakes, the shift occurring in the season when fish larvae are abundant. Our results have shown that predation by the larval fish would control not only the abundance, but also the community structure of the small-sized zooplankton prey.