Variation in otolith elemental fingerprints was investigated in albacore tunas (Thunnus alalunga) sampled in the southwest Indian Ocean (SWI) and along the Atlantic coast of South Africa (SA). A total of 72 otoliths were selected, from 46 adult fish captured around the Reunion Island (SWI) and 26 juvenile and sub-adults sampled at two locations off the South African coast (SA-N and SA-S, n = 13 per location). LA-ICP-MS was used to assess the signatures in 15 chemical elements at all otolith cores (to investigate potential differences in fish spawning origin among regions) and along all otolith edges (to characterize the chemical signatures of fish capture areas). Among the 15 chemical elements analysed, only Mg, P, Zn, Sr, Ba, B and Cu were above detection limits and significantly contributed to the variation in otolith composition. Based on differences in these elements, two groups of distinct multi-elemental signatures, denoting potentially discrete spawning origins (SpO), were identified at the otolith cores using hierarchical clustering based on Euclidian distances. Each of the two potential SpO contributed to the tuna sampled in all three areas, suggesting a common origin in some fish caught in the Atlantic and in the Indian Ocean and important trans-oceanic migrations between these two Oceans. The possible location of the two spawning areas is discussed based on the signatures recorded on the otolith edges before the final capture of the fish, in both oceans. This study was part of a collaborative project on the population structure of tuna, billfish and sharks of the Indian Ocean (PSTBS-IO).