The aboriginal populations living in the Nicobar Islands are hypothesized t
o be descendants of people who were part of early human dispersals into Sou
theast Asia. However, analyses of ethnographic histories, languages, morpho
metric data, and protein polymorphisms have not yet resolved which worldwid
e populations are most closely related to the Nicobarese. Thus, to explore
the origins and affinities of the Nicobar Islanders, we analyzed mitochondr
ial DNA (mtDNA) hypervariable region I sequence data from 33 Nicobarese Isl
anders and compared their mtDNA haplotypes: to those of neighboring East As
ians, mainland and island Southeast Asians, Indians, Australian aborigines,
Pacific Islanders, and Africans. Unique Nicobarese mtDNA haplotypes, inclu
ding five Nicobarese mtDNA haplotypes linked to the COII/tRNA(Lys) 9-bp del
etion, are most closely related to mtDNA haplotypes from mainland Southeast
Asian Mon-Kmer-speaking populations (e.g., Cambodians). Thus, the dispersa
l of southern Chinese into mainland Southeast Asia may have included a west
ward expansion and colonization of the islands of the Andaman Sea.