Nase (Chondrostoma nasus) and common barbel (Barbus barbus) are two rheophilic cyprinid fish naturally present in the Belgian Meuse and Rhine basins. During the last decades, the construction of dams together with changes in hydrological regimes, modifications of riverbed morphology and water pollution have caused some local dramatic declines in their populations. However, recent improvements in terms of water quality and habitat fragmentation allow considering as realistic a rational restocking plan of locally endangered patrimonial fish species such as nase and common barbel. Restocking operations for a conservation purpose have to be based on the knowledge and the use of wild type genetic strains. Therefore, the aim of this study was to characterize the genetic structure and diversity of nase and common barbel populations in South Belgium rivers. Wild common barbels (n = 313) and nases (n = 271) were sampled by electrofishing in respectively 10 and 6 different tributaries from the Meuse and Rhine rivers. Genotyping was performed on 24 microsatellite markers for each species. Preliminary results showed, for both species, a differential genetic clustering between fish originating from the Meuse basin and those originating from the Rhine basin. Detailed analysis describing the genetic structure and diversity of South Belgium populations will be presented and will serve as a management tool to set up a breeding plan for conservation restocking.