We describe a reliable and relatively inexpensive method for detecting and differentiating between the commonly studied avian blood parasite genera Haemoproteus, Plasmodium, and Leucocytozoon. The assay takes advantage of a Haemoproteus-specific restriction site identified by sequencing full mitochondrial genomes from two Haemoproteus and three Plasmodium lineages and an adjacent, genus-specific restriction site identified in Leucocytozoon spp. The assay was sensitive to simulated parasitemias of approximately 8 × 10−6 per erythrocyte and was 100% accurate in differentiating between parasite genera isolated from a broad geographical and taxonomic sampling of infected hosts.

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