Plasmodium coatneyi is a simian malaria parasite with various biological features similar to the human malaria P. falciparum and potential as a model for severe cases of malaria. We have characterized two single-copy genes from P. coatneyi, the circumsporozoite protein and merozoite surface protein-9 genes, and determined its phylogenetic relationship among Plasmodium species. This study demonstrates that while it has similarities to P. falciparum, P. coatneyi belongs to a distant clade including several simian malaria parasites and the human malaria P. vivax. P. coatneyi forms a monophyletic group with P. knowlesi, demonstrating their close relationship despite some very distinctive biological characteristics.