The study of the Portuguese marine ichthyofauna has a long historical tradition, rooted back in the 18th Century. Here we present an annotated checklist of the marine fishes from Portuguese waters, including the area encompassed by the proposed extension of the Portuguese continental shelf and the Economic Exclusive Zone (EEZ). The list is based on historical literature records and taxon occurrence data obtained from natural history collections, together with new revisions and occurrences. It comprises a total of 1191 species, distributed among 3 superclasses, 4 classes, 42 orders, 212 families and 617 genera. If considering only the EEZ and present territorial waters, this list represents an increase of 230 species (27.8%) and of 238 species (29.0%), when compared to the information available in FishBase (2012) and in the last checklist of marine and estuarine fishes of Portugal (1993), respectively. The order Perciformes shows the highest diversity, with 54 families, 162 genera and 299 species. Stomiidae (80 species), Myctophidae (71 species) and Macrouridae (37 species) are the richest families. From the listed species, 734 are present off mainland Portugal, 857 off the Azores and 766 off Madeira. Within the limits of the examined area, three species are reported for the first time in mainland Portugal and twenty-nine records are identified as doubtful. A total of 133 species have been recorded from the extended Portuguese continental shelf (2 off mainland Portugal, 117 off the Azores and 14 off Madeira), two of which are common to the Azores and Madeira extensions. Biogeographically, the Atlantic group is the most important (548 species – 46.01%), followed by the Lusitanian group (256 species – 21.49%), the African group (71 species – 5.96%), the Boreal group (34 species – 2.85%), the Mediterranean group (31 species – 2.60%), the Macaronesian group (21 species – 1.76%), the Atlantic/African group (19 species – 1.60%) and the Mediterranean/African and the Arctic groups, each with only 1 species (0.08%). Regarding the preferences for vertical habitat, the demersal fishes are the most important group (305 species – 25.61%), followed by the mesopelagic group (228 species – 19.14%), the bathypelagic group (164 species – 13.77%), the benthopelagic group (147 species – 12.34%), the bathydemersal group (115 species – 9.66%), the reef-associated group (88 species – 7.39%), the pelagic group (74 species – 6.21%), the epipelagic group (58 species – 4.87%) and 1 species (0.08%) of the benthic group. The oceanic habitat is the best represented group comprising 446 species (37.45%), followed by the shelf group (199 species – 16.71%), the slope group (164 species – 13.77%), the inner shelf group (89 species – 7.47%), the coastal group (70 species – 5.88%), the outer shelf group (29 species – 2.43%) and the oceanic/shelf group (7 species – 0.59%).