We performed a phylogenetic analysis, based on the partial small subunit rRNA gene (SSU rRNA) sequences from 13 apicoplasts (including new sequences of Sarcocystis muris and Hyaloklossia lieberkuehni) and 16 other plastids, with cyanobacteria as an outgroup. The apicoplast sequences formed a highly supported monophyletic clade with two distinct clades, representing coccidia and haemosporidia, with coccidia divided into Eimeriidae and Sarcocystidae subclades. We confirmed the phylogenetic position of H. lieberkuehni within the Sarcocistidae, as a sister to the Toxoplasma/Neospora group. The coccidian plastid sequences appear to evolve slowly, while their homologues from haemosporidians are more rapidly evolving. We suggest that the higher evolutionary rate is reflected by the increase in the AT content and the possible reduction of the outer apicoplast membrane in some haemosporidians. Since the apicoplast SSU rRNA gene sequences, when compared with their nuclear homologues, offer a higher number of informative positions, they can be used for phylogenetic inference within the Apicomplexa.