1. Supportive breeding programmes are becoming increasingly crucial for the conservation of many declining freshwater fishes such as the European common nase, Chondrostoma nasus. However, small relict populations are genetically highly vulnerable, and supportive breeding can have a detrimental impact on the genetic composition of the cultured offspring (e.g. as a result of inbreeding, genetic drift, and adaptation to captivity).2. This study monitored the genetic effects of a continuing supportive breeding programme of common nase by comparing the genetic diversity of two wild spawning populations with the respective wild offspring and the progeny from captive breeding originating from spawners of the two wild populations, considering genetic variability, genetic differentiation, and inbreeding effects using nine microsatellite markers.3. Despite low genetic differentiation, the offspring from captive breeding and from one of the natural populations (River Sims) were remarkably different genetically, as indicated by pairwise analyses of genetic divergence (F ST from 0.028 to 0.070; Jost's D EST from 0.080 to 0.205) and the discriminant analysis of principal components. The mean number of alleles and mean allelic richness in the captivebred offspring and also in the wild offspring of the River Sims were lower than for wild populations of spawners and natural offspring of the River Mangfall, and signs of inbreeding effects were detected (F = 0.106 for captive bred and 0.048 for natural offspring). 4. The observed effects can probably be attributed to the limited number of spawners (two females and three males) used for captive breeding. In addition, the results support previous evidence on recruitment problems of the Sims population, such as a reduced hatching success. 5. Collecting fertilized eggs from the wild and rearing them in captivity (repatriation approach) could be an alternative to stripping a limited number of spawners and thereby to improve the conservation of genetic diversity of natural populations.