This study aimed to evaluate the importance of inshore estuarine habitats for the maintenance of offshore exploited stocks of the horse-eye jack Caranx latus , a marine tropical species of high economic value. Otoliths of 143 yearlings were used to develop a data set of multi-elemental fingerprints for different juvenile habitats of C. latus in northeastern Brazil, including 7 estuaries and the coastal zone. This data set was then compared to the signatures in the juvenile part of the otolith of 40 sub-adult and adult fish caught at sea to identify their origin. Although otolith multi-elemental concentrations overlapped for some of the estuaries investigated, the maximum overall discrimination accuracy between them was only 58%. However, grouping several estuaries according to their similarity in elemental signatures increased accuracy to 80%. In both cases, correct re-assignment rates for the coastal zone were above 94%, and strontium (Sr) was the most significant element in juvenile habitat discrimination. The remaining elements (B, Ba, Co, P, Rb, and Zn) allowed us to distinguish between 3 distinct groups of estuaries, for which correct re-assignment rates were 70-88%. Juvenile fingerprints in sub-adult and adult otoliths revealed that most of the fish in the local, exploited stock (75%) originate from an inshore estuarine habitat, particularly from larger estuaries under constant marine influence (32.5%). This biological connectivity between continental and coastal waters should be considered for the conservation of tropical marine coastal stocks in general, as it is likely to apply to other exploited marine species, in Brazil and elsewhere.