Biogeography is known to have shaped the diversity and evolutionary history of avian haemosporidian parasites across the Neotropics. However, a paucity of information exists for the temperate Neotropics and especially from nonpasserine hosts. To understand the effect of biogeography in the temperate Neotropics on haemosporidians of nonpasserine hosts we screened ducks (Anseriformes) from central Chile for the presence of these parasites. Forty-two individuals of 4 duck species (Anas flavirostris, Anas georgica, Mareca sibilatrix, Spatula cyanoptera cyanoptera) were collected and assessed for haemosporidian parasite infections by real-time polymerase chain reaction screening and subsequent sequencing of the mitochondrial cytochrome b gene. Haemoproteus (subgenus Haemoproteus) and Plasmodium were detected in 2 host species, A. georgica and S. c. cyanoptera, with no Leucocytozoon found. Overall haemosporidian prevalence was low (14.2%), with the prevalence of Plasmodium (11.9%) being substantially greater than that of Haemoproteus (4.8%). Six haemosporidian cytochrome b lineages were recovered, 2 Haemoproteus and 4 Plasmodium, with all 6 lineages identified for the first time. In phylogenetic reconstruction, the Chilean Plasmodium lineages were more closely related to South American lineages from passerine birds than to known lineages from anseriforms. The subgenus Haemoproteus known from nonpasseriformes has never been identified from any anseriform host; however, we recovered 2 lineages from this subgenus, one from each A. georgica and S. c. cyanoptera. Further work is needed to determine if this presents true parasitism in ducks or only a spillover infection. The results of phylogenetic reconstruction demonstrate a unique evolutionary history of these Chilean parasites, differing from what is known for this host group. The unique geography of Chile, with a large part of the country being relatively isolated by the Atacama Desert in the north and the Andes in the east and south, would present opportunities for parasite diversification. Further work is needed to investigate how strongly the biogeographical isolation has shaped the haemosporidian parasites of this area. Our results add to the growing body of evidence that nonpasserine hosts support unique lineages of haemosporidian parasites, while also demonstrating the role of biogeography in haemosporidian parasite diversity in the temperate Neotropics.