Demersal zooplankton (DZ) appear in the water column at night, and are highly abundant in mangrove, seagrass, and coral reef habitats; however, few studies have discussed their role in aquatic food webs, considering different consumers and their preferences on different DZ' size classes. This study elucidates the role of DZ as a food source for higher trophic levels in an estuarine area, particularly with respect to the food preference and size selection of their consumers. The study was conducted in the mangrove forest of Fukido Estuary and an adjacent reef lagoon (with seagrass-dominated and seagrass-coral mixture areas) on Ishigaki Island, Japan. The abundance of demersal zooplankton was 4.0, 5.4, and 11.3×10 4 ind.m -2 for seagrass, mangrove, and seagrass-coral mixture habitats, respectively. The lowest DZ biomass was recorded in mangroves and mainly dominated by smaller organisms, because their consumers in this habitat prefer large-sized prey. The δ 13 C and δ 15 N signatures showed that, in mangroves, demersal zooplankton constituted a higher proportion of the diet of fishes than in lagoon habitats; however, demersal zooplankton did not have a significant role in the diet of fishes and macroinvertebrates in the lagoon. Consistency among biomass, stomach contents, and the proportions of DZ of all size classes in the diet of mangrove fishes indicated that DZ serve as a major food source. In contrast, fishes in lagoon habitats consumed more crabs, shrimps and mollusks than DZ. In conclusion, our analytical approach allowed us to demonstrate that DZ of different body sizes serve as food sources for different consumers in different habitats of the estuarine ecosystem.