Tharus--a population of Terai (a region with a severe malarial morbidity in the past)--can be subdivided into three main groups: Western, Central and Southern Tharus. They have usually been considered a Mongoloid population and this has been further substantiated by mtDNA findings on Central Tharus. Studies on the distribution of malaria-related genes have shown an extremely high frequency (0.8) of the alpha-thal gene among Western and Central Tharus. This frequency, however, unexpectedly turned out to be only 0.04 in a sample of Eastern Tharus. This raised doubts on the common notion that Tharus are a single anthropological entity. In the present investigation mtDNA markers were studied in the same sample of Eastern Tharus previously examined for the alpha-thal gene. The findings were: 1. the same three features which confirmed the classification of Central Tharus as Mongoloids (i.e., the common occurrence of HpaI-1/HincII-1 and HaeII-5 morphs, and the lack of BamHI polymorphism) were also present in this sample. Since the only neighbouring population accessible to Tharus, until recently, has been Hindu (Caucasoids), this result strongly supports the notion that Tharus are indeed a single anthropological entity; 2. two statistically significant differences between Eastern and Central Tharus--namely, a much higher HaeII morph 5 frequency among Central Tharus, and the absence in the same group of the mutation at 15.487 bp (very common among Eastern Tharus)--together with the results on alpha-tal gene, suggested that Tharu subgroups underwent an effective reproductive isolation.