Sergestid shrimps of the genus Acetes are important in global shrimp fisheries and nearshore food-webs. The feeding habits of the sympatric species Acetes erythraeus and A. intermedius from Panguil Bay, Philippines were studied using gut contents and stable isotopes analyses. Both species are omnivorous suspension feeders of plankton, macrophyte detritus, and amorphous particulate organic materials. However, the diet of adults and juveniles differed by prey type. Gut fullness differed over 24 h with a night-time peak in A. erythraeus and morning and midnight peaks in A. intermedius. Over 1 year gut fullness peaked during July to September for both species, with a minor peak during January for A. intermedius. Stable isotope analysis revealed similar d15N values, but both species showed ontogenetic and interspecific separation of d13C. A. erythraeus seemed to assimilate highly depleted carbon food sources by mangrove-based detrital and plankton trophic pathways, whereas A. intermedius relied on plankton and macroalgal and seagrass detrital pathways. These trophic differences may be mechanisms of partitioning the feeding niche, but allotopy in the two species with A. erythraeus confined to more brackish waters and A. intermedius dwelling in more saline marine waters may indicate that habitat niche segregation underlies these contrasting carbon trophic pathways.