The purpose of this research was to test traditional phylogenetic hypotheses regarding protozoan parasites of the phylum Apicomplexa Levine, 1970 using sequences from the nuclear small subunit ribosomal RNA (SSU rRNA) genes in addition to phenotypic characters. A phylogenetic reconstruction of the order Haemosporina based on ultrastructural and life cycle characters indicated that a clade containing the genera. 'Haemoproteus, Hepatocystis', and 'Polychromophilus' was the sister group to the genus ' Plasmodium'. There was a general agreement between the parasite phylogeny and that of the dipteran definitive hosts. In a study of the coccidia, the SSU rRNA genes of several tissue cyst-forming coccidia were amplified by PCR, cloned, and sequenced. Phylogenetic analysis of the sequences demonstrated that 'Isospora' spp. without Stieda bodies are more closely related to the genera 'Toxoplasma' and 'Neospora'. These groups all form a sister clade to the genus 'Sarcocystis'. The results have important taxonomic implications as all 'Isospora ' spp. have usually been grouped with the distantly related genus ' Eimeria'. By contrast, 'Isospora' spp. with Stieda bodies grouped within an eimeriid clade, indicating that the genus ' Isospora' as classified by some authors is polyphyletic. The phylogenetic relationships among neogregarine and eugregarine parasites of invertebrates were also inferred using SSU rRNA sequences. The results from these analyses indicate that both the eu- and neogregarines are basal to the other apicomplexans, a grouping consistent with most previous assessments. The genus 'Cryptosporidium ' has closer phylogenetic affinities with the gregarines than with the coccidia, indicating that 'Cryptosporidium' is not a true coccidian as indicated by most classifications. The SSU rRNA gene sequences from various apicomplexan parasites as well as from definitive and intermediate hosts were also used as data for phylogenetic analysis of both groups. There was no pattern of cospeciation of parasites with vertebrate hosts. Host switching of several parasite clades to similar vertebrate intermediate hosts has occurred throughout their evolution. A closer pattern of coevolution with definitive hosts is apparent as piroplasms appear to have coevolved with ticks, haemosporinids coevolved with dipterans, and gregarines coevolved with insects, annelids, and similar invertebrate hosts.