Background The low prevalence of blood parasites in some bird species may be related to the habitats they frequent, the inexistence of the right host-parasite assemblage or the immunological capacity of the host. Here, we assess the parasite load of breeding populations of Eleonora's falcon (Falco eleonorae), a medium-sized long-distance migratory raptor that breeds on small isolated islets throughout the Mediterranean basin and overwinters in inland Madagascar. Methods We examined the prevalence and genetic diversity of the blood parasites belonging to the genera Plasmodium, Haemoproteus and Leucocytozoon in Eleonora's falcon nestlings from five colonies and in adults from two colonies from nesting sites distributed throughout most of the species' breeding range. Results None of the 282 nestlings analysed were infected by blood parasites; on the other hand, the lineages of Plasmodium, Haemoproteus and Leucocytozoon were all found to infect adults. Our results support the idea of no local transmission of vector-borne parasites in marine habitats. Adult Eleonora's falcons thus may be infected by parasites when on migration or in their wintering areas. Conclusion The characteristics of marine environments with a lack of appropriate vectors may thus be the key factor determining the absence of local transmission of blood parasites. By comparing the parasite lineages isolated in this species with those previously found in other birds we were able to infer the most likely areas for the transmission of the various parasite lineages.