The pelagic fishery of Lake Tanganyika, which is largely made up of the three species Lates stappersii, Limnothrissa miodon, and Stolothrissa tanganicae, has been in decline, and there is no clear understanding of the primary underlying causes. It has been suggested that climate change has altered the primary productivity of the system, but detailed knowledge of the system's food web is required to elucidate the effect on higher trophic levels. The aim of this study is to determine the diet of the three commercially important fish species. Muscle tissue samples for stable isotope analysis were taken from February through April 2017, supplemented with stomach samples from L. stappersii for use in stomach content analysis. The stomach analysis showed an ontogenetic change in the diet composition of L. stappersii, shifting from copepods to fish larvae, supplemented with shrimp, to whole fish prey as the fish grew larger. Stable carbon and nitrogen isotope values from fish muscle were consistent with this observation, and also seemed to indicate that fish of similar sizes had similar diets, irrespective of species. This suggests that the diet of the pelagic fish species might be better explained by size, rather than species. The isotope data revealed a short range of δ15N values from primary consumers to fish, which may help explain the high fisheries productivity of Lake Tanganyika, and the strong impact of primary productivity changes on fisheries yield.