Abstract: Plecoglossus altivelis is an important rare economic fish distributed along Chinese,Japanese and Korean coasts.In the present study,genetic diversity of hatchery and wild population was compared.A 445 bp fragment of control region was obtained.The haplotype diversity(0.198 4±0.092 4)and nucleotide diversity(0.000 8±0.000 9)of hatchery population were obviously lower than those of wild population(h=0.810 5±0.067; π=0.002 6±0.002 0).Great differentiation was detected between these two populations(F_st=0.447,P=0.000).The topology constructed by neighbour-joining tree indicated no significant genealogical structures for two populations.Individuals from Japan showed a distant relationship with individuals from China.Mismatch distribution analysis indicated that P.altivelis may have experienced a recent population expansion.The present study indicated that current genetic situation of hatchery and wild populations was not optimistic.