Compsura is a genus of freshwater fish belonging to the order Characiformes and the family Characidae, subfamily Cheirodontinae. The type species, Compsura heterura, was described based on specimens from the Itapicuru River, which is part of the North Group (GN) within the Northeast Mata Atlântica ecoregion (NMAF). Although the original description focused on the Itapicuru River, C. heterura has also been found in the São Francisco (São Francisco ecoregion, SF) and Parnaíba (Parnaíba ecoregion, PB) river basins. Recent studies have suggested a broader distribution in the GN of the NMAF, including the Sergipe, Vaza-Barris, and Pojuca river basins, which indicated possible historical connections between these basins and the SF, influencing species distribution. The present study aimed to investigate, describe, and analyze the phylogeographic pattern of C. heterura in the NMAF and SF ecoregions. To this end, mitochondrial COI gene sequences from samples of the species in these ecoregions were obtained and analyzed. A haplotype network was constructed and comparatively analyzed with a distribution map also developed in this study. Five haplotypes were found, all of which are exclusive to the basins where they occur. The absence of shared haplotypes indicates structuring within the species, corroborated by the number of mutational steps that separate them. This structuring is evident both between distinct ecoregions (NMAF and SF) and within the same ecoregion (NMAF). Considering that freshwater fishes tend to have their biogeographic history related to the history of the basins where they occur, the results found are as expected, since these drainages are isolated from each other.