Post-larvae of amphidromous gobies, locally known as ‘penja’ in Sulawesi, is a group of fish that are often caught by fishermen as consumption fish when migrating and has a life-cycle which begins with adults spawning in the river, the eggs and embryos are then carried by river currents, hatching before arriving at the sea, and spend their larval and postlarval phases in the sea, before returning to the river to grow and eventually reproduce. Belonging to several species, they often school together and are difficult to identify with certainty based on morphological characters. Molecular biology tools such as DNA barcoding can help overcome this challenge. This study, conducted from June 2018 to December 2019, aimed at identifying ‘penja’ post-larvae migrating upstream in the Mandar River in West Sulawesi (Indonesia) using a molecular approach. Two species were identified: the threadfin goby Sicyopterus longifilis de Beaufort, 1912, locally known as ‘penja mawassar’, and the blue neon goby Stiphodon semoni Weber, 1895, local name ‘penja alus’. Both are widespread species. Main characteristics of these species and of their fisheries are given. The determination of harvested postlarvae is a major issue for fishery management.