The diet and population structure of larval and early juvenile Glossogobius callidus and Redigobius dewaali (Gobiidae) were examined from the headwater region of the permanently open Great Fish Estuary along the south-east coast of southern Africa. Stomach contents of five selected size classes were sorted and identified to the lowest possible taxonomic level for each goby species. Using % Index of Relative Importance values, ontogenic shifts and dietary breadth were determined for each species as was dietary overlap between species. Numerically, both gobiid species showed similar temporal and spatial trends. Seasonal differences in catches were evident, although no numerical differences across sampled sites were found. A large degree of dietary overlap was found between the two species. The zooplanktonic diet showed a greater degree of ontogenic shift in R. dewaali than G. callidus, although similar trends were found for both. In both goby species, Calanoid sp. (Copepoda) generally decreased in importance across size classes, being the most important in the smallest size class whilst Corophium sp. (Amphipoda) increased in importance across size classes, being the least important at the smallest size classes. For both G. callidus and R. dewaali, Insecta contributed significantly to at least one of the five size classes. The larger size classes showed the least dietary overlap and the highest niche breadth. In addition, as is the case in many gobiids worldwide, the larger size classes of both sampled gobiid species consumed a broader prey size range. In conclusion, dietary overlap was largely similar between the young gobiids, suggesting that either food resources are not limiting, or niche separation is attributed to differences in foraging strategies. Ontogenic dietary shifts were however present for both gobiids with regard to prey items and prey size, suggesting a greater degree of foraging niche separation in adults of the species.