Phylogenetic analyses of several marker genes have previously shown that Asian primate Plasmodium species (malaria parasites) were monophyletic including Plasmodium vivax, one of the four malaria parasites that infect humans. However, except for the presence of a few established groupings, phylogenetic relationships among the Asian primate Plasmodium species + P. vivax group have neither been clearly resolved with confident statistical supports, nor the closest relative to P. vivax was elucidated. Since comparative biological studies between P. vivax and its closest relative would provide valuable information on immunopathogenesity of vivax malaria, the phylogenetic positions of P. vivax in the clade comprised of Asian primate Plasmodium species are crucial. In order to clarify the phylogeny and evolution of Asian primate Plasmodium species including P. vivax, we obtained sequences of apicoplast genome-encoded genes for small subunit rRNA (SSUrRNA), large subunit rRNA (LSUrRNA), and caseinolytic protease C (ClpC) from 10 Plasmodium species: P. vivax, P. coatneyi, P. cynomolgi, P. fieldi, P. fragile, P. hylobati, P .inui, P. knowlesi, P. simiovale, and P. gonderi. Together with published sequences of apicoplast genome-encoded elongation factor Tu (EF-Tu) from these species, we performed phylogenetic analyses of a combined 4-gene data set using P. gonderi, an African old world monkey parasite, as an outgroup. The ML phylogeny based on a 'concatenate model' for combining information of the 4 genes clearly revealed close relationships between P. vivax and P. cynomolgi and monophyly of P. fragile with the P. coatneyi/P. knowlesi clade. When 'separate' models were assumed for combining phylogenetic information from the 4 genes that were independently analyzed, the support for the P. vivax/P. cynomolgi clade was substantially decreased, but the monophyly of P. fragile with the P. coatneyi/P. knowlesi clade was still robustly confirmed. The present analyses place P. fragile in a position that is incongruent with the early branching status of P. fragile amongst P-vivax-related primate Plasmodium species propose by Escalante et al. (Proc Natl Acad Sci USA 2005 102: 1980).