Domestically reared introduced (or escaped) individuals can have detrimental genetic effects on the indigenous populations into which they are released. Consequently, numerous studies have attempted to estimate whether non-native specimens have contributed to the gene pool of wild populations. So far, the key limiting factor of such studies has been their lack of appropriate baseline genetic material. Here, microsatellite DNA analyses of historical scale samples and contemporary wild and introduced populations were used to assess spatiotemporal population structure and stocking effects among endangered Lake Saimaa (eastern Finland) grayling (Thymallus thymallus, Salmonidae). Significant decreases in genetic differentiation were detected between wild and introduced populations since the commencement of stocking in 1986. Accordingly, up to 15% of the contemporary wild grayling were confidently identified to be of pure hatchery origin, and recent hybridization between the hatchery and indigenous individuals appeared likely. Despite these clear genetic imprints of stocking, the contemporary populations exhibited evolutionary relationships congruent with the sampling locations, and up to 73% of contemporary individuals were identified to be of pure indigenous origin. The use of historical baseline material should prove efficient for monitoring gene flow between domesticated and wild populations in other species also, e.g. salmonids, game animals and plants.