Channa lucius (Cuvier, 1831) is one of the endangered and economically important species in Channidae family with high potential for aquaculture in the Mekong Delta. Limited genetic information has hindered the conservation and domestication programs of this species. The present study used inter-simple sequence repeats (ISSR) markers to assess the genetic diversity of C. lucius. Samples were collected from three conservation locations (Ca Mau, Kien Giang and Long An) and one from inland fisheries areas (Can Tho) in the Mekong Delta. Eight highly polymorphic markers yielded 76 scorable bands from 93 samples (22 to 24 samples per population) with the size range from 450 to 2000 bp. Results revealed high levels of genetic diversity of C. lucius populations with unbiased expected heterozygosity from 0.250 to 0.271 and Shannon index from 0.364 to 0.395, in which those from Ca Mau population were lowest. Nei's genetic distance between populations ranged from 0.022 to 0.057 with low overall genetic difference G_ST = 0.090 and high gene flow (Nm = 5.06), indicating that C. lucius populations were not subdivided. This study provides useful information for conservation projects of C. lucius in the region