Amazonian rivers have been more frequently conceptualised as barriers rather than as habitats for birds with their own ecological and biogeographic histories. However, many river-restricted bird species have differentiated within the formidable network formed by the Amazon and its tributaries. Here we demonstrate that the riverine-distributed Crimson-fronted Cardinal ( Paroaria baeri ) is narrowly distributed along the middle Rio Araguaia basin, where it comes into contact and hybridises with the geographically widespread Red-capped Cardinal ( P. gularis ). This one-dimensional hybrid zone, which is situated over ca .160 km along the Araguaia and Javaés Rivers, appears to be of recent origin. Admixed individuals between the non-sister P. baeri and P. gularis are phenotypically intermediate between the parental species, and superficially resemble the geographically disjunct and phylogenetically distant Masked Cardinal ( P. nigrogenis ). Two phenotypically admixed specimens were confirmed as such based on sequences of the mitochondrial Cytb and the Z-linked MUSK gene. Field observations and genetic data indicate that P. baeri × P. gularis hybrids are capable of producing viable offspring, but more data are necessary to confirm hybrid viability and fertility. The non-sister hybridising species P. baeri and P. gularis last shared a common ancestor 1.8–2.8 mya (uncorrected genetic p-distance of 4%), which corresponds closely to when the Araguaia/Tocantins river basin last discharged directly into the Amazon.