Version of record in Molecular Ecology Resources:  https://doi.org/10.1111/1755-0998.13402 The Maroni is one of the most speciose basins of the Guianas and hosts a megadiverse freshwater fish community. Although taxonomical references exist for both the Surinamese and Guyanese parts of the basin, these lists were mainly based on morphological identification and there are still taxonomical uncertainties concerning the status of several fish species. Here we present a barcode dataset of 1,284 COI sequences from 199 freshwater fish species (68.86% of the total number of strictly freshwater fishes from the basin) from 124 genera, 36 families, and 8 orders. DNA barcoding allowed for fast and efficient identification of all specimens studied as well as unveiling a consequent cryptic diversity, with the detection of 20 putative cryptic species and 5 species flagged for re-identification. In order to explore global genetic patterns across the basin, genetic divergence landscapes were computed for 128 species, showing a global trend of high genetic divergence between the Surinamese south-west (Tapanahony and Paloemeu), the Guianese south-east (Marouini, Litany, Tampok, Lawa…), and the river mouth in the north. This could be explained either by lower levels of connectivity between these three main parts or by the exchange of individuals with the surrounding basins. A new method of ordination of genetic landscapes successfully assigned species into cluster groups based on their respective pattern of genetic divergence across the Maroni Basin: genetically homogenous species across the basin were effectively discriminated from species showing high spatial genetic fragmentation and possible lower capacity for dispersal.