The Northeastern Mata Atlântica freshwater ecoregion (NMAF) includes part of the eastern Brazilian coastal drainages, has high level of fish endemism and great biogeographic significance. A taxonomic inventory of freshwater fishes from 25 drainages of the NMAF ecoregion and a biogeographic analysis using the Parsimony Analysis of Endemicity (PAE) method were carried out. A total of 192 native species was listed. The PAE method was applied to 24 basins and 37 species, resulting in five equally parsimonious area diagrams. The strict consensus diagram indicates the existence of two main groups of basins throughout the NMAF ecoregion. These groups were denominated: North Group and Central-South Group. The Central-South Group shows a basal polytomy composed by two Groups (Central Group and South Group) plus the rio Itapemirim basin. The North Group is composed by eight drainages from the rio Sergipe to the rio Paraguaçu, the Central Group by five drainages from the rio Cachoeira to the rio Jequitinhonha, and the South Group by nine drainages from the rio Buranhém to the rio Doce. Comments about the species distribution and the fish fauna shared with adjacent ecoregions are provided. We also present a comparison of the hypothesis of river relationships proposed herein with published phylogenetic hypotheses that include taxa relevant to this study.