The oldest known shipwreck in southern Africa was found in Namibia in 2008.^1–4 Forty tons of cargo, including gold and silver coins, helped identify the ship as the Bom Jesus, a Portuguese nau (trading vessel) lost in 1533 while headed to India.^4–6 The cargo included >100 elephant tusks,⁷ which we examined using paleogenomic and stable isotope analyses. Nuclear DNA identified the ivory source as African forest (Loxodonta cyclotis) rather than savanna (Loxodonta africana) elephants. Mitochondrial sequences traced them to West and not Central Africa and from ≥17 herds with distinct haplotypes. Four of the haplotypes are known from modern populations; others were potentially lost to subsequent hunting of elephants for ivory. Stable isotope analyses (δ¹³C and δ¹⁵N) indicated that the elephants were not from deep rainforests but from savanna and mixed habitats. Such habitats surround the Guinean forest block of West Africa⁸ and accord with the locations of major historic Portuguese trading ports.^9,10 West African forest elephants currently range into savanna habitats;^11–13 our findings suggest that this was not consequent to regional decimation of savanna elephants for their ivory in the 19^th and 20^th centuries. During the time of the Bom Jesus, ivory was a central driver in the formation of maritime trading systems connecting Europe, Africa, and Asia. Our integration of paleogenomic, archeological, and historical methods to analyze the Bom Jesus ivory provides a framework for examining vast collections of archaeological ivories around the world, in shipwrecks and other contexts.