Mysids are one of the most important prey items for juveniles of commercially important coastal fishes in the world. Although most of mysid species are considered as omnivorous, unidentified materials are dominant in their diets and there have been few quantitative studies on mysid food habits. The contribution of different food sources of different habitat-type sympatric mysids, epibenthic Orientomysis japonica and sand-burrowing Archaeomysis japonica, which are common in the Tango Sea, western Wakasa Bay, were determined by N and C stable isotope ratios and fatty acid (FA) biomarkers. Mysids had no markers specific to terrestrial plants and bacteria such as long-chain and odd FAs, which suggested that mysids do not use them as food sources. δ¹⁵N of both mysid species increased gradually from February (7.0‰: O. japonica, 4.8‰: A. japonica) to June (9.3‰, 8.1‰). Based on MixSIR model results, the main food sources of O. japonica changed from POM to benthic microalgae and then to zooplankton. This species exhibited a dinoflagellate marker, 22:6(n-3), as much as a diatom marker, 20:5(n-3), which indicated dinoflagellates played as an important supplemental source to mysids. Our results indicate O. japonica can respond successfully to changes of food environment by opportunistic feeding and A. japonica is less carnivorous than O. japonica.