Abstract Mangrove-fringed bays are highly variable ecosystems that provide critical habitats for fish species. In this study we assessed the fish assemblage in three mangrove-fringed bays (Punta Rocafuerte, Saca Calzón and Garrapatero) in the Southeast side of Santa Cruz Island, Galapagos Marine Reserve. Using gillnets, we carried out a total of 108 fieldtrips from January 2010 to December 2011. A total of 1 773 bony and 740 cartilaginous fishes belonging to 26 species and 15 families were identified at the same sampling sites. Species richness was higher in the protected bay (Garrapatero) than in those open to fishing (Punta Rocafuerte, Saca Calzón). Blacktip sharks (Carcharhinus limbatus, n= 729), Thoburn’s mullets (Mugil thoburni, n= 492), Peruvian mojarras (Diapterus peruvianus, n= 440), milkfish (Chanos chanos, n= 206) and the yellow fin mojarras (Gerres cinereus, n= 197) were the most common species across sites and season (cold and warm). The abundance of the most common species varied seasonally, with C. limbatus and C. chanos being more abundant in the warm season (December to April), and M. thoburni, C. limbatus and G. cinereus in the cold season (June to October). Temperature was the most important driver of abundance in C. limbatus and C. chanos, while salinity influenced Umbrina galapagorum. This study represents the first evaluation of the fish assemblage composition and dynamics in mangrove-fringed bays in the Galapagos Marine Reserve. Rev. Biol. Trop. 66(2): 674-687. Epub 2018 June 01.