Lake Tanganyika in East Africa has two primary basins (Northern and Southern) and borders four sovereign countries. Effective management of the fisheries of this lake requires sound biological understanding of the various fish stocks. The feasibility of fish stock identification within different basins and sub-basins of this lake was attempted through otolith elemental composition analysis. Element ratio signatures of whole sagittal otoliths (Mg/Ca, Sr/Ca and Ba/Ca) of two commercially important clupeid species (Stolothrissatanganicae, n=18; Limnothrissamiodon, n=32) were used to classify individual fish to their resident basins. No element ratios in L. miodon otoliths were significantly different between Southern sub-basins, yet Ba/Ca and Sr/Ca ratios were significantly different for individuals from the Northern and Southern basins. Sr/Ca and Ba/Ca ratios were also significantly different between otoliths of sympatric L. miodon and S. tanganicae in the Northern Bujumbura Sub-basin. Species differences may be due to ontogenetic and environmental variables. Sr/Ca and Ba/Ca element concentration ratios contributed greatly to basin classification of individual fish. Canonical discriminant analysis correctly classified 91% of L. miodon and 83.3% of S. tanganicae to the Bujumbura sub-basin, compared to 59.9% of L. miodon collected from the Southern Basin that were correctly classified to this basin. These classification rates are similar to those found for estuarine species. Our results of a limited study suggest that otolith element compositions can be used as a natural tag to identify fish stocks in Lake Tanganyika and assist in the implementation of a multi-national fisheries best management plan.