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The black kite Milvus migrans, one of the most common raptor species, shows great flexibility as regards food resources and breeding sites. While black kite subspecies are found all over Eurasia, Africa and Australia, it has been poorly studied outside of Europe, with virtually nothing known about the phylogeny of populations in Asia, India, Africa or Australia. We analysed 85 published black kite nucleotide sequences and ca 660 new sequences from the ranges of the main black kite subspecies using a non‐invasive method of DNA extraction from moulted feathers. In doing so, we evaluated genetic diversity and population affinities and reconstructed their demographic histories. Populations from Europe, northern Asia and India all had separate haplogroups of the mitochondrial cytochrome b gene. The European and North Asian subspecies were isolated in the Pleistocene and spread across the northern Palearctic following climate amelioration, forming a broad intergradation zone from western Siberia and Kazakhstan to eastern Europe. Representatives of the European, North Asian and Indian haplogroups were found in Pakistan, where they probably breed. The Australasian population separated from the Indian population relatively recently and carries one of the two Indian major haplotypes. We found support for the assumption that the African yellow‐billed kite differs from the black kite at the species level. Further, the yellow‐billed kite contains at least two genetically distant mitochondrial lineages with ranges that do not correspond with its traditional subspecies ranges. Based on these data, we were able to outline the general pattern of black kite phylogeography over its entire range, making it possible to evaluate the evolutionary history of the species as a whole. [ABSTRACT FROM AUTHOR]