For stock assessment purposes in the Indian Ocean, a single stock of yellowfin is considered by the Indian Ocean Tuna Commission (IOTC). However, the degree of connectivity and mixing rates are still uncertain, although this information is essential for developing effective and sustainable management strategies. This study uses otolith oxygen and carbon stable isotope composition (δ18O and δ13C) of young-of-the-year yellowfin tuna from “known” nursery areas in the equatorial Indian Ocean to establish a reference east/west baseline of isotopic signatures. This baseline was then used to determine the origin of adolescent and adult yellowfin tuna individuals captured in three fishery regions of the western Indian Ocean: R1A, R1B and R2. Results from this study suggest limited east to west connectivity of yellowfin tuna in the Indian Ocean, with west nurseries being the mayor source of contribution to the western fisheries. However, for all the three regions, we found adolescent and adult yellowfin tuna with an otolith stable isotope signal that was not characteristic of either of the two groups (east/west) present in the current baseline. This result may suggest that there is a third source of origin that is not being captured by the original baseline; being either a temporal or/and spatial component. Findings of otolith stable isotope composition of yellowfin tuna in the western Indian Ocean can provide a more comprehensive understanding of the species’ spatial structure and connectivity beyond the current assessment of a single stock in the ocean basin. To that aim, advancing collaborative scientific and sampling designs in highly migratory species such as yellowfin tuna should be encouraged.