We used screening techniques based on polymerase chain reaction (PCR) to explore the avian hematozoan parasites (Plasmodium spp. and Haemoproteus spp.) of two previously uninvestigated regions of continental South America. Comparisons of tropical-zone Guyana and temperate-zone Uruguay revealed that overall prevalence of Plasmodium and Haemoproteus species detected in a diverse sampling of potential hosts was significantly higher in Guyana. The difference in prevalence between the two geographic zones appears to be attributable to ecological differences rather than taxonomic sampling artifacts. Diversity of hematozoan haplotypes was also higher in Guyana. We found no relationship between hematozoan haplotype and host family sampled within or between regions. We found very few Plasmodium and no Haemoproteus haplotypes shared between the two regions, and evidence of geographic structuring of hematozoan haplotypes between the two regions. We suggest that a lack of hematozoan haplotype transmission between the two regions may be attributable to the migratory patterns of each region's avian hosts.