An annotated checklist of the fish species of the Madagascar EEZ (southwestern Indian Ocean) comprises a total of 1,798 species in 247 families. 158 species are recorded from Madagascar for the first time. The majority of the species is autochthonous; 28 species have been introduced, mainly in freshwater habitats. The fish fauna is mostly marine (95.4% of the total number of native fish species), with the Gobiidae, Labridae, Serranidae, Pomacentridae and Apogonidae being the families with most representatives; among the 90 native freshwater fish species (adults mainly occurring in freshwater), the Cichlidae are the dominating family, but there are also two endemic families, the Bedotiidae (16 species) and Anchariidae (6 species). The fish fauna at Madagascar is typical for offshore, high islands in the southwestern Indian Ocean. Zoogeographically, the main element of the marine fish fauna of Madagascar consists of widespread tropical Indo-Pacific species (978 species, 58.3% of the total native marine species). A total of 13 species (3.3%) are found worldwide, either circumtropical or circumtropical including warm temperate zones. A total of 215 species (12.8%) are found worldwide, either circumtropical or circumtropical including warm temperate zones. An additional 453 species (27.0%) are Indian Ocean endemics, including 233 western Indian Ocean endemics (13.9%), 73 southwestern Indian Ocean endemics (4.4%), 16 species endemic to Madagascar and Mascarenes (1.0%), 4 species endemic to Madagascar and Comoros (0.2%), 3 species endemic to Madagascar and Madagascar Ridge (0.2%), and 37 marine species endemic to Madagascar (2.2%). Most of the autochthonous freshwater fishes are endemic to Madagascar (87 species, 96.7% of the native freshwater species).

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