In the Gulf of Guinea, bigeye Thunnus obesus (BET) and yellowfin tuna Thunnus albacares (YFT) are important for commercial fisheries and play a prominent ecological role as top predators. Using fatty acid profiles and carbon and nitrogen stable isotopes we examined their niche partitioning in this understudied region. Niche overlap was high (>70%), similar to percentages in other ocean basins. BET occupied a higher trophic position than YFT and fed on deeper prey (high δ15N values and high proportions of mono-unsaturated fatty acids). The trophic position of YFT decreased slightly in the last 15 years (δ15N values decrease ~0.5 ‰) suggesting a change in epipelagic communities, as observed in the eastern Pacific Ocean. Ontogenic changes were limited to BET. For both species, the dietary proportion of the diatoms marker (20:5n-3) increased in the seasonal upwelling area, highlighting the seasonal habitat influence on tunas diet. The relatively lipid-rich muscle (~6 % dry weight) of Atlantic tropical tunas suggested a richer diet in this region than for Indian Ocean tropical tunas and/or differences in energy allocation strategies.