A molecular phylogeny of the Spizaetus cirrhatus complex is presented in this study, based on two sections of the mitochondrial genome: partial sequences of the cytochrome b gene and of the control region (CR). The topologies derived from the two sequences are in agreement. Within S. cirrhatus distances are rather low (0–1.5% in cytochrome b). Among the cirrhatus subspecies the island taxa floris, vanheurni and andamanensis form distinct haplogroups in the CR trees, conforming to the earlier subspecific divisions which were based on morphological characters. On the other hand, the most widespread subspecies, limnaeetus, does not represent a monophyletic group in the gene trees and its haplogroups do not cluster according to geographic affinities. An unambiguous resolution of relationships among haplotypes and haplogroups, respectively, was not achieved, suggesting a more recent radiation of this group of hawk-eagles in the course of the last ice ages. Concerning the outgroup taxa Spizaetus philippensis and Spizaetus lanceolatus, our data indicate a clear genetic distinction between the two subspecies S. p. philippensis and S. p. pinskeri, suggesting that they should be treated as distinct species. Yet the phylogenetic relationships of the three outgroup taxa with respect to S. cirrhatus are ambiguous in our trees. The taxonomic consequences of applying different species concepts (BSC, PSC) are discussed. The species concept chosen would result in different conservation strategies.