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Stable isotope analyses of muscle tissue (δ13Cmuscle and δ15Nmuscle) and otoliths (δ13Cotolith and δ18Ootolith) were used to retrospectively track habitat uses of Lethrinus lentjan, and to determine any association between Setiu Lagoon (nursery habitat) and coastal artificial reefs (CARs; adult habitats) on the Terengganu coast, Malaysia. Muscle stable isotopes exhibited a spatial change from inshore to offshore habitats associated with growth, possibly related to the reef-ward movement of the fish. Otolith stable isotopes of adult fish from CARs were measured in juvenile (from outside the core to the first opaque zone of otolith) and adult (the edge of otolith) portions and were compared with those of juveniles from Setiu Lagoon, suggesting that the adult fish may not primarily use the lagoon as a nursery before ontogenetically migrating to CARs. The effects of coastal currents between monsoonal seasons could reorientate offshore juvenile migration; hence, adult cohorts in CARs may be replenished from various nursery habitats along the coast. Additionally, similarities in the δ18Ootolith values of juvenile and adult sections suggested that some individuals may not spend their juvenile phases in shallow estuarine habitats. Based on the findings of this study, we recommend that coastal conservation strategies take into account multiple nursery habitats rather than a single one.