<p>The correct understanding of fish population structure plays a positive role in their fishery management. The dotted gizzard shad, <i>Konosirus punctatus</i>, is widely distributed in the coastal waters of the northwestern Pacific. With the over-exploitation of economically important fishes, its importance is increasingly prominent. To further examine the population genetic structure of <i>K. punctatus</i> across the northwestern Pacific, the amplified fragment length polymorphism (AFLP) and the inter-simple sequence repeats (ISSRs) were employed to perform genetic variation analysis. The results showed that the combination of polyacrylamide gel electrophoresis and silver staining can effectively detect genetic variation for <i>K. punctatus</i> populations. The average proportions of polymorphic loci were 46.26% and 87.13% for AFLP and ISSR markers, respectively, and the genetic diversity parameters showed no obvious differences among populations. Both analysis molecular variance (AMOVA) and pairwise <i>F</i>_st suggested that there was significant genetic differentiation between Chinese and Japanese populations. All samples also clustered into two clades based on the unweighted pair-group method analysis (UPGMA) tree by two markers, which indicated significant genetic differentiation among populations. Consistent with the previous studies, there are two highly differentiated groups at the nuclear gene level and they were suggested to be treated as two separate genetic management units. The results of the present study could provide the genetic management strategy for this important economic species.</p>