This study was carried out to determine the amphipod fauna in Mar Piccolo, Mar Grande and the Gulf of Taranto. Material in this study was obtained from 96 stations at different depths (maximum depth: −50 m) using various methods depending on the substrata. A total of 65 species was determined and 25 species are new records in the seas of Taranto. Microdeutopus gryllotalpa, Ericthonius brasiliensis, Monocorophium insidiosum, Elasmopus rapax, Gammarus aequicauda, Gammarus insensibilis, Leucothoe spinicarpa, Lysianassa costae and Pseudoprotella phasma were the dominant species and have been found in all areas considered. The comparison of the data shows that the area examined presents a high difference regarding biocenotic index. The highest number of species was collected in the Gulf with 1944 individuals, belonging to 58 species and 19 families, followed by Mar Grande with 1448 individuals belonging to 36 species and 11 families; finally Mar Piccolo with 698 individuals, 12 species and 6 families, in the First Inlet and 546 individuals, 18 species and 6 families, in the Second Inlet.