Analysis of the hybridisation events between two Iberian Chondrostoma species in the Távora River (Douro Basin) suggests different levels of trait introgression. Nuclear traits studied showed different introgression levels, whereas mitochondrial DNA introgression was not found. Lack of mtDNA introgression suggests that male and female hybrids may not equally fit or that possibly backcross matings may not be random. This could be contributing to the maintenance of a relative morphologic cohesion of hybridizing species, in spite of differences relative to allopatric populations. The hybrid zone was possibly originated by secondary contacts between populations of the species involved, motivated by connectivity between adjacent basins. Reanalysis of the hybridizing taxa revealed that Chondrostoma macrolepidotum is the species involved in the interspecific crosses with C. duriense, instead of C. arcasii as previously proposed.