The genus Dactylogyrus represents the species richest group within the family Dactylogyridae (Monogenea). In our study, we aimed to study the composition of Dactylogyrus communities in two cyprinid fish species, Barbus meridionalis and B. barbus, forming the hybrid zone in southern France. Over the period 2007-2013, 327 fish were dissected for metazoan parasites in both sympatric and allopatric Barbus populations. Fish determination was performed using 30 microsatellite markers and revealed the occurrence of 40 hybrid individuals in seven Barbus populations. Of all parasites, Dactylogyrus species represent the most dominant group in almost all studied populations. D. carpathicus parasitized both Barbus species, while D. malleus was specific for B. barbus. These parasites reached the highest values of abundance and prevalence in allopatric B. barbus populations. D. dyki was present solely in allopatric population of B. meridionalis that is in disagreement with previously published data. Furthermore, D. extensus (specific to Cyprinus carpio) represented a rare species firstly detected in B. meridionalis individuals. Overall, significant trend towards higher abundance of Dactylogyrus parasites in B. barbus compared to both B. meridionalis and hybrids was detected. Further extensive sampling of sympatric populations is required to investigate the composition of Dactylogyrus communities along the Barbus hybrid zone.