Adults of the fish-borne intestinal trematode species Haplorchis taichui were collected from humans in three provinces of Vietnam: Ha Giang, Thanh Hoa and Quang Tri. Genetic analysis revealed three groups of the parasite from clustering dendrograms, correlating with the localities in which they were collected. Measurements of evolutionary divergence over sequence pairs were greater between the different populations than within them, which indicated that the three populations were genetically different. The significance (Fst= 0.73; P value < 0.05) of the genetic variation of the three studied populations implied that genetic separation of the populations had already occurred, which may have been caused by a low gene flow among the different H. taichui populations. Factors contributing to the low gene flow may include isolation resulting from the intermediate-host fish rarely being sold outside of the rural commune where they are raised and the enclosed aquacultural areas themselves.