Abstract: This work was carried out from the assessment of the conservation status of the freshwater ichthyofauna from Bahia State. The inventory data and species distribution were obtained from the specialized scientific literature and representative ichthyological collections. A total of 281 native species was recorded in Bahia State, distributed in the Northeastern Mata Atlantica (NMA) and São Francisco (SFR) freshwater ecoregions. There was a larger number of species in the NMA (187 spp.), composed by several coastal basins, than in the SFR (134 spp.), composed by São Francisco river basin. Among the 30 families recorded, Characidae and Rivulidae were the most representative, with 53 and 48 species, respectively. The conservation status of 214 species was assessed and 33 of them (15%) were included in the IUCN threat categories. Of these, 11 species were classified as vulnerable (VU), 12 as endangered (EN), and 10 as critically endangered (CR). Most threatened species (n = 14) belongs to the family Rivulidae. The larger number of threatened species in the NMA: (n = 23) is mainly related to the high endemism of restricted-range species associated with the human occupation impacts along the coastal regions. In the SFR, most of threatened species are annual killifishes, which are locally disappearing due to increasing degradation of their temporary habitats.