We collected zooplankton from May to October, 2011, with the aim of understanding the zooplankton community distribution and food web interaction between the open water and littoral (aquatic plants) zones in two small reservoirs with different land covers (Sobudang, Myeongdong). Small-sized reservoirs are more abundant in South Korea, and a total of 51 and 65 species of zooplankton were identified at the two small reservoir (Sobudang and Myeongdong), where zooplankton densities were more abundant in the littoral zone than in the open water zone. Cladocerans and copepods densities were also higher in the littoral zone, in contrast, rotifers showed higher densities in the open water zone (t-test, P/0.05). Epiphytic zooplankton dominated at the littoral zone (Lecane, Monostyla, Alona and Chydorus) because aquatic plants provided refuge spaces for attachment. Some rotifers (e.g. Brachionus, Keratella and Polyarthra) were more abundant in the open water zone because of their small size, which might help them to go unnoticed by predators. In two-way ANOVA, rotifers related to two reservoirs or habitat space (littoral zone and open water zone), but cladocerans and copepods showed a statistically significant relationship on only two reservoirs. The results of stable isotope analysis showed that zooplankton in the littoral zone tended to depend on organic matter attached to aquatic plants as a food source, which indicates the avoidance of competition of zooplankton with other macro-invertebrates (e.g. Damselfly larva, Cybister brevis and Neocardina denticulate). As a result, zooplankton community distribution is determined by not only habitat space (aquatic plant zone and open water zone) but also by food source (phytoplankton).