Frozen blood samples from 13 species of free-ranging birds (n = 65) and captive Chilean flamingos (Phoenicopterus chilensis) (n = 46) housed outdoors in the Chicago area were screened for Plasmodium. With the use of a modified polymerase chain reaction, 20/65 (30.8%) of free-ranging birds and 26/46 (56.5%) of flamingos were classified as positive for this parasite genus. DNA sequencing of the parasite cytochrome b gene in positive samples demonstrated that eight species of free-ranging birds were infected with five different Plasmodium spp. cytochrome b lineages, and all positive Chilean flamingos were infected with Plasmodium spp. cytochrome b lineages most closely related to organisms in the Novyella subgenus. These results show that Chilean flamingos may harbor subclinical malaria infections more frequently than previously estimated, and that they may have increased susceptibility to some Plasmodium species.