The genetic diversity and population structures within and between Korean and Japanese populations of Salanx ariakensis were investigated using AFLP (amplified fragment length polymorphism). Using seven primer pair sets, 411 fragments were amplified from 31 specimens of S. ariakensis, 393 fragments (96%) being polymorphic. The expected heterozygosities were 0.211 and 0.245 for the Japanese and Korean populations, respectively, levels similar to those of other freshwater and diadromous fishes, but lower than those of marine fishes. The difference in genetic diversity between the two populations may result from their different habitat sizes. Principal coordinate analysis using 393 polymorphic fragments resulted in specimens from each population being plotted separated, suggesting an absence (or little if present) gene flow between them since Tsushima Strait has been open. Therefore, each population of S. ariakensis is relevant from the conservation perspective and should at least be treated as a "management unit" for conservation purposes.