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In a previous study of Southeast Asian genetic variation, we characterized mitochondrial DNAs (mtDNAs) from six populations through high-resolution restriction fragment length polymorphism (RFLP) analysis. Our analysis revealed that these Southeast Asian populations were genetically similar to each other, suggesting they had a common origin. However, other patterns of population associations also emerged. Haplotypes from a major founding haplogroup in Papua New Guinea were present in Malaysia; the Vietnamese and Malaysian aborigines (Orang Asli) had high frequencies of haplogroup F, which was also seen in most other Southeast Asian populations; and haplogroup B, defined by the Region V 9-base-pair deletion, was present throughout the region. In addition, the Malaysian and Sabah (Borneo) aborigine populations exhibited a number of unique mtDNA clusters that were not observed in other populations. Unfortunately, it has been difficult to compare these patterns of genetic diversity with those shown in subsequent studies of mtDNA variation in Southeast Asian populations because the latter have typically sequenced the first hypervariable segment (HVS-I) of the control region (CR) sequencing rather than used RFLP haplotyping to characterize the mtDNAs present in them. For this reason, we sequenced the HVS-I of Southeast Asian mtDNAs that had previously been subjected to RFLP analysis, and compared the resulting data with published information from other Southeast Asian and Oceanic groups. Our findings reveal broad patterns of mtDNA haplogroup distribution in Southeast Asia that may reflect different population expansion events in this region over the past 50,000–5000 years.