Stable carbon and nitrogen isotope ratios were used to elucidate primary carbon sources and trophic relationships of the fish and shrimp community in the Klong Ngao mangrove ecosystem, southern Thailand. There were no significant differences in isotopic compositions of biota between mangrove and offshore sites (Welch-Aspin test). The δ15N values of eight fish species and two shrimp species at both sites were also not significantly different by the test, meaning that at both sites they feed on the same diets due to the discharge of large quantities of mangrove sediments. The δ15N isotopic enrichment of consumers suggested that there are four trophic levels in the Klong Ngao food web, with at least two fish species capable of switching feeding strategies and thus altering their apparent trophic positions. Phytoplankton culture experiments indicated that mangrove-derived sediments could play an important role in stimulating phytoplankton growth for low turbidity offshore areas, thus providing an alternate food source. The isotopic associations among sources and consumers indicated that mangroves were the major carbon source supporting aquatic food webs in the Klong Ngao ecosystem.