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Conservation of genetic variability is of priority for hatchery stocks employed to supplement natural populations. Supportive breeding of Atlantic salmon is carried out in order to enhance wild populations at the south of the European distribution (northern Spain). In this study we demonstrated that adult breeders chosen for creating hatchery stocks by artificial spawning preserved all genetic variants present in wild Spanish populations for six microsatellite loci. However, significant losses of genetic variability were found in juveniles released to the native rivers. An inadequate strategy of crosses was the cause of genetic variation decrease in these hatchery stocks. Unbalanced sex ratio was identified as one of the causes of genetic erosion. Increasing the number of breeder males was suggested to maximize fidelity of hatchery stocks to native wild genetic patterns.