The high prevalence of Duffy negativity (lack of the Duffy blood group antigen) among human populations in sub-Saharan Africa has been used to argue that
Plasmodium vivax
originated on that continent. Here, we investigate the phylogenetic relationships among 10 species of
Plasmodium
that infect primates by using three genes, two nuclear (β-tubulin and cell division cycle 2) and a gene from the plastid genome (the elongation factor Tu). We find compelling evidence that
P. vivax
is derived from a species that inhabited macaques in Southeast Asia. Specifically, those phylogenies that include
P. vivax
as an ancient lineage from which all of the macaque parasites could originate are significantly less likely to explain the data. We estimate the time to the most recent common ancestor at four neutral gene loci from Asian and South American isolates (a minimum sample of seven isolates per locus). Our analysis estimates that the extant populations of
P. vivax
originated between 45,680 and 81,607 years ago. The phylogeny and the estimated time frame for the origination of current
P. vivax
populations are consistent with an “out of Asia” origin for
P. vivax
as hominoid parasite. The current debate regarding how the Duffy negative trait became fixed in Africa needs to be revisited, taking into account not only human genetic data but also the genetic diversity observed in the extant
P. vivax
populations and the phylogeny of the genus
Plasmodium