Haemosporidian parasite diversity among raptorial birds (hawks and owls), as estimated by DNA sequencing, is proving to be greater than previously anticipated from taxonomic assessments based on parasite morphology. Here, we place raptor parasites in a phylogenetic context, including new parasite cytochrome b (cyt b) sequences from North America and Europe and from a variety of host species not previously sampled. Mitochondrial DNA sequences reveal raptor-specific parasite clades within Parahaemoproteus, but not within Plasmodium. We also recovered a strikingly divergent clade of raptor parasites that aligns with neither genus, but groups with both as a sister clade to Leucocytozoon. Different cyt b primer sets recovered additional sequences from 3 of these samples, which grouped with Parahaemoproteus in 2 cases and with Plasmodium in 1 case. Possible explanations (after excluding contamination) include multiple infections, alternative cyt b copies within the mitochondrial genome, and nuclear copies of mitochondrial genes. We believe the latter 2 explanations are unlikely because these divergent cyt b lineages form a single clade and were also recovered with several additional genomic markers.