Stable carbon and nitrogen isotope ratios of benthic invertebrates and their potential food sources, such as suspended particulate organic matter (POM), benthic microalgae, attached algae and seagrass, were identified in Dong-dae Bay during the winter. The carbon stable isotope ratios demonstrate that filter feeders, such as oysters (−19.5 ± 1.0‰), use benthic microalgae (−21.2 ± 0.2‰) as a major food, and polychaetes such as Glycera spp. (−14.0 ± 0.6 ‰) preferentially use meiofauna, such as nematodes (−14.0 ± 0.4‰) and copepods (−13.3 ± 1.0‰). These meiofauna may feed on mixed resources (including bacteria) with the isotope ratios between benthic microalgae (−21.2 ± 0.2‰) and seagrass (−9.3 ± 01.0‰). These findings are consistent with the trophic enrichment in the nitrogen isotope ratios (by 3–4‰) between consumers and food sources. Moreover, the results of the MixSIR model based on the observed isotope ratios suggest a large seagrass contribution to the food sources of benthic organisms such as meiofauna (~53.7–62.6%) and macrobenthos (~41.1–68%) through the food web. This model additionally suggests a relatively large contribution of benthic microalgae to the food sources of filter feeders (i.e. 26.4% for oysters).