To clarify potential trans-oceanic connectivity and variation in the natal origin of albacore tuna (Thunnus alalunga) from the southwest Indian Ocean (SWI) and the southeast Atlantic (SA), lifetime otolith elemental signatures were assessed from 46 adults sampled from Reunion Island, and 26 juveniles(group 2+) sampled from two locations along the Atlantic coast of South Africa. LA-ICP-MS analysis was used to assess the multi-elemental composition in B, Ba, Mg, P, Sr, and Zn along the otolith edge (chemical signatures of the capture area), but also near the otolith primordium (spawning origin) and in an area located at 1400–1600 µm from it (nursery origin). Two groups of distinct near-primordium multi-elemental signatures, denoting potentially discrete spawning origins (SpO), were identified using hierarchical clustering. Each of the two SpO was found to contribute to the albacore stocks from all the areas sampled, suggesting a common spawning origin in some fish from the SWI and from the SA, and complex migrations between the two oceans. Three potentially discrete primary nursery sites were identified, each contributing to SA juvenile and SWI adult capture sites differently. The timing for the trans-oceanic movements observed for each albacore capture zone and its implications for local stock management are discussed.