Natal origin and stock structure of bigeye tuna (Thunnus obesus) in the Indian Ocean were investigated using trace elements in otoliths. Otoliths were collected from (i) young of the year (YOY) bigeye caught in the west central and north east regions of the Indian Ocean, which are known to be spawning areas, and (ii) older fish in the south west and south east regions of the Indian Ocean. Otoliths were analysed by LA-ICP-MS at two points: near the core and at the edge, providing an elemental signal from material deposited while the fish were close to their spawning grounds and from material deposited while they were in or close to their capture areas, respectively. Twelve elemental isotopes were measured: Li, Na, Mg, P, K, Mn, Fe, Cu, Zn, Rb, Sr, Ba. Core and edge signatures for the same otolith were significantly different for most elements. Core signatures did not differ significantly for YOY bigeye in the west and east northern locations; this suggests that the ocean chemistry did not differ significantly between these locations. The core signatures for older fish in the west and east southern locations did not differ significantly from each other, but they did differ significantly from the core signatures observed for fish from the northern spawning locations, indicating either: (i) the fish from the southern locations were not spawned in either of the northern locations; or (ii) they were spawned in one of the northern locations but the ocean chemistry was very different in the years they were spawned. Core and edge signatures for the same otolith were significantly different and edge signatures also did not differ between fish from the two northern locations. While temporal variability in otolith elemental chemistry may confound spatial structure information, these results show that otolith chemistry can differentiate separate groups of bigeye within the Indian Ocean. Analysing YOY from known spawning areas over several years would set up a baseline for matching otolith cores from older fish collected in other areas of the Indian Ocean that may then provide evidence of population structuring.