The spectrum of mitochondrial DNA (mtDNA) variation in India clearly supports the African origin of modern humans. In their deepest branching points Indian mtDNA clusters share common combinations of mutations with clusters specific for eastern and western Eurasian populations. However, their further diversification appears to be specific to India. The sub-clusters of haplogroup U in India and in Europe overlap only at the basis of the multifurcation. Also the structure of Asian dominant haplogroup M in India differs profoundly from that of other Asian populations. Around 10% of Indian mtDNAs are found around a phylogenetically crucial node—R*—which is ancestral to more than 90% of typically European mtDNAs and also to a portion of Asian specific mtDNA lineages such as haplogroups B and F. Coalescence estimates, calculated separately for these three major clusters in India, indicate a major radiation of mtDNA lineages starting approximately 50,000 years ago. The fraction of lineages attributable to a recent influx of maternal genes either from eastern or western Eurasia is below 10%. Furthermore, their spread does not correlate with the spread of the Sanskrit-and Dravidian-based languages in India.