Abstract A total of 92,934 fish larvae representing 19 families were sampled monthly from the Sangga Kecil estuary (Matang Mangrove Forest Reserve) and adjacent coastal waters from May 2002 to October 2003. Larval fish assemblages were numerically dominated by Gobiidae (50.1%) and Engraulidae (38.4%). Canonical Correspondence Analysis (CCA) revealed that the larval fish assemblages, including their ontogenetic stages, differed between the mangrove estuary and adjacent offshore waters, and that salinity, turbidity and zooplankton food are the major environmental factors structuring the larval fish assemblages. Estuarine preflexion gobiid larvae were ubiquitous in the coastal and estuarine waters. Larval stages of euryhaline species that were spawned in offshore waters, such as Engraulidae and Clupeidae, were largely advected into mangrove areas at the postflexion stages. Larvae of other euryhaline fishes (Sciaenidae, Blenniidae and Cynoglossidae) that may have been spawned inside the estuary were, however, exported to offshore waters. Given that the collective number of juvenile and adult fish families in the Matang estuary was 53, while the number of larval families was only 17, the former is quite disconnected from the existing larval fish population in the estuary.