Abstract
Isozymes and mitochondrial DNA (mtDNA) were used as genetic markers to evaluate the reproductive success of transplanted stocks of ayu Plecoglossus ultivelis in a highly stocked Japanese river, the Shinano. Two major alleles at the MPP and GPI‐A* loci and 26 mtDNA clonal genotypes were demonstrated and surveyed in two non‐native source populations and five collections from the Shinano River. Contributing populations were clearly discriminated in their isozymes and mtDNA composition. Despite the stocking of large numbers of non‐native fish, they have had little effect on the genetic characteristics of the native population. Maturation and migration of the stocking and native populations was traced by genetic markers to clear the mechanism of this event. All the contributing populations join together in the migration toward the spawning ground throughout the spawning season but these contributing populations occur independently of each other in other sites of the river.