This dataset comprises information on the zoological collections gathered by Portuguese oceanographic campaigns in colonial territories during the 1950–60s, currently deposited in the Museu Nacional de História Natural e da Ciência (MNHNC), Universidade de Lisboa (UL). The collection has a complex institutional background starting with the creation of the Missão de Estudos de Pesca de Angola (MEPA, 1951–1953) and its evolution to the Missão de Biologia Marítima (MBM, 1953–1966), the creation of the Centro de Biologia Piscatória (CBP, 1959–1966), and its transformation into the Centro de Biologia Aquática Tropical (CBAT 1966–1974). This dataset comprises 7305 occurrence records representing more than 30000 specimens of marine fauna from 11 countries. The collection has a wide taxonomic coverage, holding representatives of 1372 species, belonging to 447 families and 21 different classes across 7 phyla, with particular focus on fishes, mollusks and decapod crustaceans. The bulk of this material was collected between 1952 and 1965 in Angola, Cape Verde and Mozambique, often aboard the Oceanographic Vessel “Baldaque da Silva”.