Parotocinclus includes 27 species of small armored catfish that occur in coastal river basins of Brazil, and also in the São Francisco river basin (SF). Four species occur exclusively in the SF: P. cearensis, P. jumbo, P. prata and P. robustus. Recent sampling in a tributary on the right bank of the São Francisco river revealed a population distinct morphologically from the congeners known to the basin. An integrative taxonomic study, using morphological and molecular data, revealed it as a new species. Parotocinclus sp. n. differs from its congeners, except P. bidentatus, P. cabessadecuia, P. jacumirim, P. muriaensis, P. pukuixe, P. seridoensis and P. spilurus, by its vestigial or rudimentary adipose fin (vs. developed adipose fin). The new species differs from P. bidentatus and P. muriaensis by the absence of accessory unicuspid teeth (vs. presence), from P. jacumirim and P. seridoensis by the abdomen being completely covered with large plates (vs. an abdomen with small plates and naked areas in P. jacumirim and P. seridoensis, and an abdomen with small plates without naked areas in P. pukuixe), from P. spilurus by the pectoral girdle being completely covered by odontodes (vs. the pectoral girdle being covered solely laterally by odontodes), and from P. cabessadecuia by having rounded white spots on the head (vs. an absence of white spots). The phylogenetic results based on molecular data indicate that Parotocinclus sp. n. is a sister taxa of P. jacumirim and both are closely related to a clade that includes P. bahiensis and P. minutus, but distant from P. maculicauda, the type species of the genus. The molecular results showed a clear structuring of Parotocinclus sp. n., supporting the hypothesis of a new species indicated by the morphological analyses.