We analyzed the small subunit ribosomal RNA (SSUrRNA) gene sequences from 13 malaria species parasitic to humans, chimpanzees/gorillas, Old World monkeys, rodents, birds, and lizards in order to reconstruct the phylogenetic relationships among the Plasmodium species. The SSUrRNA genes of Plasmodium vivax and P. ovale were sequenced by the dideoxy method in our laboratory; other sequences were retrived from GenBank. These sequences were aligned with the SSUrRNA gene sequence of outgroup species, Paramecium and Toxoplasma. After gaps and ambiguous regions were deleted, the aligned sequences were used for phylogenetic analysis by maximum likelihood and distance methods. The tree defines two major clades, the first with the bird and reptile parasites, the second with the rest of the species. The two bird parasites, P. gallinaceum and P. lophurae, do not closely cluster with human, chimpanzee/gorilla, Old World monkey, or rodent parasites, but cluster with the lizard parasites. P. vivax clusters with three Old World monkey parasites, P. cynomolgi, P. fragile, and P. knowlesi in decreasing order of closeness. P. ovale, while in a separate clade, is more closely related to P. vivax than to P. malarie or P. falciparum. P. malariae and P. berghei do not closely cluster with any of the other clades or with each other. Statistical analysis proves that the placement of P. falciparum in the bird malaria clade is less likely than in the mammalian malaria clade. Our analysis reveals that: (1) human malaria parasites have an evolutionary independent origin; (2) P. falciparum is most closely related to P. reichenowi and did not arise from lateral transfer of a bird parasite, as was previously suggested; and (3) the lizard malaria parasites are true members of the genus Plasmodium.