Sarcocystis muris is a coccidium with a two-host life cycle involving the domestic cat and the mouse, Mus musculus. S. muris and Theileria annulata belong to the phylum Apicomplexa, but the latter organism is a tick-borne protozoon in the subclass Piroplasmea and causes tropical theileriosis in cattle. The small-subunit ribosomal RNA (16S-like rRNA) coding regions of these organisms as well as that of the free living dinoflagellate Crypthecodinium cohnii were amplified using polymerase chain reaction techniques and compared to 16S-like rRNA sequences from other eukaryotes. The 16S-like rRNA genes of S. muris and T. annulata are more similar to each other than either is to Plasmodium falciparum, the cause of malignant tertian malaria of humans or Plasmodium berghei, the agent of the commonly studied malaria of rodents. Evolutionary trees inferred from the rRNA sequence similarities support a close phylogenetic relationship between the Apicomplexa and Dinoflagellata as represented by Prorocentrum micans and C. cohnii. Apparently members of these related phyla arose from an ancestral stock that gave rise to the ciliated protozoa.