Increasingly sophisticated taxonomic tools have enhanced our understanding of species diversity and phylogenetic relationships in elasmobranchs. Nevertheless, ichthyologists continue to face challenges in resolving the taxonomic placement and authentication of some taxa, particularly those originally described based on morphology. The recently described genus Fontitrygon comprises several Atlantic dasyatid stingrays whose phylogenetic positions have remained unresolved due to the lack of molecular data. In this study, we employed an integrative taxonomic approach to identify and determine the phylogenetic position of the understudied Fontitrygon garouaensis from Nigeria. Specimens were collected from freshwater ecosystems along the Jebba and Lokoja stretches of the River Niger in Nigeria. Comparative morphological analysis distinguished F. garouaensis from other Fontitrygon species by the presence of a depressed central-spine shaft with flanges extending along either side, a flattened oval disc, an obtuse snout, a whip-like tail bearing a sting, a broad and elongated snout, small pelvic fins, and radially arranged pectoral fins. Additionally, morphological measurements of the newly collected F. garouaensis were consistent with those of the syntype and holotype, confirming species identification. Phylogenetic analyses based on mitochondrial cytochrome c oxidase subunit I gene sequences recovered Fontitrygon as a monophyletic lineage and identified F. garouaensis as the sister taxon to F. margarita and F. margaritella. This study provides an integrative taxonomic assessment of F. garouaensis, clarifying its species identity and confirming the presence of F. garouaensis from the upstream of the Jebba stretch of the River Niger. We, therefore, propose an update to its IUCN geographic range.