This study evaluated levels of genetic diversity of L. chrysophekadion, one of the important migratory cyprinid species in the Mekong River using inter-simple sequence repeat (ISSR) markers. Fish samples were collected from four populations comprising three populations in the Mekong Delta of Viet Nam (An Giang, Can Tho and Dong Thap provinces) and one population in Lao PDR. Seven ISSR primers were selected to analyze 90 individuals (19-24 individuals/ population), yielding 275 bands (sizes from 400 bp to 2,900 bp). Results showed that four populations of L. chrysophekadion had high levels of genetic diversity with the percentage of polymorphic loci from 81.7–85.9%, expected heterozygosity 0.276–0.306, number of effective alleles 1.47–1.54, and Shannon index 0.415–0.451. Four populations in Laos and Viet Nam had low genetic differentiation (Nei’s genetic distance range: 0.016 – 0.022), suggesting a long migratory distance, approximately 1,200 km, of this species.