Abstract Philornis Meinert 1890 (Diptera: Muscidae) is a genus of flies that parasitize birds in the Neotropical region. The characteristics of the host–parasite interactions and its consequences may depend on the Philornis species involved, and thus precise identification of these parasites is crucial for the interpretation of ecological and epidemiological studies. However, morphological identification of Argentine Philornis species is elusive while molecular evidence points towards the existence of a complex of cryptic species or lineages undergoing a speciation process, which were named the ‘ Philornis torquans complex’. Herein the authors extended the current knowledge on the systematics and biogeography of parasitic Philornis flies from Argentina, analysing samples collected in several ecoregions, including the Atlantic Forest, Iberá Wetlands, Open Fields and Grasslands, Espinal, Pampa, Dry Chaco, Humid Chaco, Delta and Paraná River Islands, Monte of Plains and Plateaus. The results of the present study strengthen the evidence on previously described Philornis genotypes using four genetic markers (ITS2, COI, ND6, 12S rRNA). The authors report new patterns of occurrence and describe the presence of a novel genotype of subcutaneous Philornis . In addition, the present study unveils ecological niche differences among genotypes of the Philornis torquans complex in southern South America.