The mitochondrial genome is more conserved in apicomplexan parasites  than in others metazoan eukaryotes. Cytochrome b gene is, therefore, a good marker to establish phylogenetic relationships between parasites that diverged several millions years ago .
The presence of a major division within haemosporidian parasites separating mammal and sauropsid hosts, suggests that parasites of these two vertebrate groups evolved separately. In the mammalian clade of parasites, except for P. falciparum, all primate Plasmodium species share a common ancestor, although host shifts occurred during the course of primate speciation. Indeed, wild primate populations are potential reservoirs for human malaria parasites  and host shifts have occurred in Southeast Asia with, for example, Plasmodium knowlesi, which usually infect macaques, afflicting humans . Recently evidence on the origin of P. vivax as a macaque monkey malaria parasite in Southeast Asia has been proposed [7, 21]. In addition, Plasmodium simium and Plasmodium brasilianum, two species infecting South American platyrrhini primates, are genetically indistinguishable from P. vivax and P. malariae, respectively, and may have been associated with a human-platyrrhini host-switch [8, 21]. Further, haemosporidian parasite isolated from Hipposideros larvatus clusters with a baboon Hepatocystis. This association between bat and primate parasites has been previously proposed based on mitochondrial data, where a Hepatocystis species isolated from a bat (Cynopterus brachyotis, Family Pteropodidae) clusters with this baboon Hepatocystis . Needless to say, this result is not congruent with mammal phylogeny  and suggests a host switch from primates to bats.
In the sauropsid clade, the evolutionary history of Plasmodium that infects birds and lizards is not resolved. The parasite phylogeny clearly does not fit with the host phylogeny. Plasmodium parasites from birds and lizards are known to show little host specificity . Previous conclusions support that infrequent and unpredictable host shifts have occurred in the parasite-host sauropsid system . Surprisingly, the Haemosporidia isolated from Megaderma spasma in Cambodia falls within the sauropsid Plasmodium clade. However, phylogenetic relationships between the parasites of Megaderma and sauropsids are not completely resolved.
Furthermore, closely related haemosporidian parasites isolated from Myotis goudoti and Miniopterus manavi, two endemic Malagasy bat species and the haemosporidian parasite from the Cambodian Kerivoula hardwickii, all of which are placed in the family Vespertilionidae, fall within the sauropsid Plasmodium clade. This result clearly does not fit with vertebrate phylogeny and supports host switching from birds to bats. The haemosporidian vespertilionid parasites from Madagascar and Cambodia are monophyletic, which suggest that the host switching took place in the early evolutionary history of these bats and was followed by subsequent radiation and co-speciation. This is the first report showing host switching in haemosporidian parasites between birds and mammals (bats).
After rodents, bats are the largest order of mammals (at least 1,100 species, more than 20% of extant mammal species). The Chiroptera are very diverse and they are distributed almost worldwide and have extremely diverse life history traits and morphology. Based on recent molecular work, they are classified into four super-families that apparently diversified in different areas during the early Eocene as a "Big Bang" radiation  coincident with the peak of Tertiary insect diversity . In developing echolocation and different flight strategies, the ancestors of modern bats colonized various ecological niches , where birds and their associated blood parasites are thought to have been present, thus favoring host switching from birds to bats. Furthermore, Myotis goudoti and Miniopterus manavi often share common day roost sites in tree hollows, caves and rock shelters , which expose considerable numbers of densely packed individuals to the same potential blood parasite vectors.