Freshwater habitats in Indo-Pacific tropical islands are mainly inhabited by amphidromous fish, which display a marine larval phase while the rest of their life cycle takes place in rivers. Gobiidae are the most diversified fish component in these ecosystems. In this study, we focused on the status of the widespread Stenogobius genus (Gobioidei). This genus, composed of 28 presumably valid species, is distributed from the Indian Ocean to French Polynesia. This paper focuses on the revision of the Stenogobius genus based on 318 specimens, including morphomeristic data and mitochondrial COI sequences. Our results show that there is one main widespread species, Stenogobius genivittatus (Valenciennes, 1837), found in the Indo-Pacific area from the South African East coast to East Pacific locations. We redescribe this species and we state on 12 species names as synonyms of S. genivittatus.