Sixty-five Taenia samples were collected from patients in a referral hospital in Hanoi, north Vietnam, for species identification by morphological and molecular techniques. PCR-RFLP of a mitochondrial 12S rDNA fragment, developed for this study, allowed direct differentiation between all Taenia spp., overcoming the disadvantages of classical morphological examination, which failed on disintegrated samples. Taenia saginata asiatica was the most common species (55.4%) followed by T. saginata (38.5%) and T. solium (6.2%). This report demonstrates the complexity of the epidemiology of Taenia spp. in Vietnam and the need for further work to reveal transmission patterns of these species.