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A checklist of fishes recorded from Mar Muerto, La Joya-Buenavista, and Los Patos-Solo Dios lagoon-estuarine systems, northeastern Gulf of Tehuantepec, Mexico is presented. Fish samples were collected through 34 stations using several kinds of fishing gear, between April 2007 and May 2016. The checklist includes 2 classes, 19 orders, 52 families, 87 genera, and 120 species. The best-represented families are Carangidae (9 species), Gerreidae (7), and Engraulidae (6). The Mar Muerto system had 89 species, followed by La Joya-Buenavista with 76; in Los Patos-Solo Dios, only 41 species were recorded, perhaps due to a lower marine influence. Based on their ecological affinities, 43% of the fishes belong to marine stenohaline component, 42% to the marine euryhaline component, 11% are of freshwater derivation, and 5% are estuarine residents. The ichthyofauna showed high affinities to the Panamic province (80.7%) followed by Mexican (79.8%) and Cortés (73.1%) provinces. Nine species (8 native and 1 exotic) are added to the known continental fish fauna of the state of Chiapas.