The aims of the study were (1) to describe the Dactylogyrus communities living on selected South European Barbus species, (2) to analyse morphometric variability of their attachment and reproductive organs, and (3) to perform molecular phylogenetic analyses, in order to investigate the mode of speciation in Dactylogyrus species parasitizing congeneric hosts. In Bulgaria, Dactylogyrus crivellius, D. dyki and D. petenyi were found on B. balcanicus, and D. dyki on B. cyclolepis. In Spain, Dactylogyrus carpathicus and D. dyki were detected on B. meridionalis. Morphometric analyses of D. dyki revealed significant differences in the attachment and reproductive organs when individuals from different Barbus species were compared. Two monophyletic groups were recognized from the molecular phylogenetic analyses: the first included D. carpathicus and D. crivellius which have large body size and anchors, with a weakly supported basal position of D. malleus from B. barbus; the second included D. dyki and D. petenyi which have small body and anchor sizes. The comparison of host and parasite phylogenies did not indicate the intrahost speciation. Intraspecific molecular variability was found between individuals of D. dyki and D. carpathicus from different Barbus species, suggesting the need for a taxonomic revision for these species.