The natural resources of the Mekong river are extremely rich but remain poorly known and hence managed. Inland fisheries is a major source of protein and income in Cambodia, but is under growing pressure due to overfishing and habitat destruction. We study the genetic diversity and structure of two typical migratory catfishes of the Mekong river: Pangasius bocourti and Pangasianodon hypophthalmus. The population dynamic and genetic information should assist fisheries management.