Genetic variability and population structure of 11 natural ayu, Plecoglossus altivelis populations and one hatchery stock were assessed by starch gel electrophoretic analysis with 10 enzyme coding loci. Three loci were polymorphic (lower than 0.95 in major allele frequency) in natural populations,2 loci in hatchery stock. The average number of alleles per locus was 1.38. Observed heterozygosities ranged from 0.0235 to 0.088 (0.055 on the average) in natural population while 0.0925 in hatchery stock. The genetic distance among natural populations measured 0.000047-0.005407 and no significant differentiation was observed among them. On the other hand, a signifcant genetic distance was found between natural populations and the hatchery stock with measuring 0.002032-0.O08605. The results in this study suggest that the hatchery stock has diverged from natural populations, and also that careful to maintain sustainable and effective population size (parents number) should be made.