The stock unit used in fisheries resource assessment and management is generally based on the morphological and genetic characteristics of a particular population or species to avert problems caused by the treatment of multiple populations as one stock, which can lead to the overestimation of population sizes and genetic pollution. Furthermore, since the linkage of microhabitats is an important factor affecting the reproduction of marine organisms in coastal areas, an understanding of the food web in each microhabitat is essential to establish sustainable fisheries management practices. We investigated spatial variations in the food sources and feeding habits of immature stage of Siganus javus using genetic population analyses and stable isotope analyses (δ13C and δ15N). These species are commonly harvested by small-scale fisheries, and it inhabits Bandon Bay in the Surat Thani Province of Southern Thailand. Genetic variation within sampling sites was greater than that between sites. The δ13C values of S. javus differed between sites, which suggest that the different ecological habitats exhibit different rates and patterns of carbon flow even among sites located in the same bay. Our results suggest that studies combining genetic population analyses and stable isotope analyses are required to confirm the delineation of fine-scale management units intended for the development of coastal fishery resources.