Oxygen stable isotope in otoliths (δ18O) was used to investigate stock structure of yellowfin tuna (Thunnus albacares) across the Indian Ocean. Differences in otolith δ18O signatures among young of the year (YOY) yellowfin tuna were examined to determine whether there was sufficient distinction among three main nursery areas of the equatorial Indian Ocean (West, Central and East), to establish a reference isotopic signature (a baseline). The nursery origin of juvenile yellowfin (47-75 cm fork length (FL)) tuna from Reunion and Pakistan was then compared with these nursery signals. Juvenile fish from Reunion show δ18O signatures comparable with those of the nearest nursery area (West nursery), but juvenile fish from the Pakistan show distinctive δ18O composition compared to any of the nursery areas described. Therefore, samples from Pakistan were considered as an additional baseline signature for adult assignment purposes. Quadratic discriminant function analysis was used to assign adult individuals to one of the four areas in our baseline. Results indicate that western nursery was contributing the most to the fish analysed (24 adult out of 39 were predicted to this nursery) with a minor contribution from Pakistan (5 individuals). No Central or East nursery origins were detected among the adult sample. A fraction of yellowfin tuna (11 individuals) was left unclassified. This is an important first step towards understanding the mixing rates and the connectivity of yellowfin tuna in the Indian Ocean.