A better understanding of the stock structure of yellowfin tuna (Thunnus albacares) in the Indian Ocean is needed to ensure the sustainable management of the fishery. In this study, carbon and oxygen stable isotopes (δ13C and δ18O) and trace elements (138Ba, 55Mn, 25Mg and 88Sr) were measured in otoliths of young-of-the-year (YOY) and age-1 yellowfin tuna collected from the Mozambique Channel and north-west Indian Ocean regions. Elemental profiles showed variation in Ba, Mg and Mn in YOY otolith composition, but only Mn profiles differed between regions. Differences in YOY near-core chemistry were used for natal-origin investigation. Ba, Mg and Mn were sufficiently different to discriminate individuals from the two regions, in contrast with carbon and oxygen stable isotopes. A linear discriminant analysis resulted in 80% correct classification of yellowfin tuna to their natal origin. Classification success increased to 91% using a random forest algorithm. Finally, a unique larval source was detected among age-1 yellowfin tuna. The signal of these fish resembled that of YOY from a north-west Indian Ocean origin, highlighting the importance of local production. The present study supports the use of otolith chemistry as a promising approach to analyse yellowfin stock structure in the Indian Ocean.