Background: Numerous studies have been undertaken to improve knowledge on apicomplexan parasites infecting vertebrates, including humans. Of these parasites, the genus Plasmodium has been most extensively studied because of its socio-economic and public health impacts. In non-human vertebrates, studies on malaria or malaria-like groups have been conducted but information is far from complete. On Madagascar, recent studies on bat blood parasites indicate that three families, namely Miniopteridae, Rhinonycteridae, and Vespertilionidae, are infected by the genus Polychromophilus with pronounced host specificity: Miniopterus spp. harbor P. melanipherus, while Myotis goudoti is infected by P. murinus. However, most of the individuals analyzed in these previous studies were sampled on the western and central portions of the island. The aims of this study are 1) to add new information on bat blood parasites in eastern Madagascar and 2) highlight biotic and abiotic variables driving prevalence across the island. Results: In total, 222 individuals belonging to 17 bat species were analyzed. Polychromophilus infections were identified in two families: Miniopteridae and Vespertilionidae. Molecular data showed that Polychromophilus spp. parasitizing Malagasy bats form a monophyletic group composed of three distinct clades displaying marked host specificity. In addition to P. melanipherus and P. murinus, hosted by Miniopterus spp. and Myotis goudoti, respectively, we report a novel Polychromophilus lineage detected from a single individual of S. robustus. Based on the present study and the literature, different biotic and abiotic factors are shown to influence Polychromophilus infection in bats, which is correlated based on MaxEnt modeling. Conclusion: The present study improves our knowledge on Polychromophilus infecting Malagasy bats and highlights the existence of a novel Polychromophilus lineage. Additional studies are needed to get additional representatives of this novel lineage to resolve its taxonomic relationship with known members of the genus. Further, the transmission mode of Polychromophilus in bats as well as its potential effect on bat populations should be investigated to complement the results provided by our modeling and eventually provide a comprehensive picture of the biology of these host-parasite interactions.