Marine drifting animals — zooplankton — play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans, and others. Zooplankton are generally considered passive drifting organisms homogeneously distributed throughout waters, where high dispersal is expected. Although empirical observations have demonstrated that many species possess active swimming mechanisms that generate metacommunities with high beta diversity, the role of animal sizes in the process of marine zooplankton community dynamics remains unexplored. Here, we collected a total of 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients and performed metatranscriptome analyses. The samples were collected in two transects (from nearshore to offshore) twice a day (morning and night). Sample size fraction was the only variable that rendered apparent differences in species composition between the samples. Our results demonstrate differential dispersal through the size fractions — smaller size fraction communities had higher compositional homogeneity than larger ones. Contrary to expectation, distance to shore had no significant influence on the composition or diversity of zooplankton communities. This study offers novel insights on the use of metatranscriptomics for analyzing community structures and the role size plays for the marine zooplankton community assembly processes.