Falconiformes include most of the predatory birds, they play crucial role in maintaining the balance of ecology system. To further illustrate the phylogenetic status for the species of Falconiformes, the entire mitochondrial DNA (mtDNA) genome of Falco naumanni was amplified and sequenced, further phylogenetic analysis was performed by incorporating with other 8 entire mtDNA genomes representing 8 species of predatory birds by taking the Apus apus and Haematopus ater as out-groups. Our results indicated that the mtDNA genome of F. naumanni includes 17,370 base pairs in length, which has the similar organization and gene order with other mtDNA genomes of the species belonging to Falconiformes. Further phylogenetic analyses supported that the F. naumanni clustered with other species of Falconidae, which formed the sister group of Accipitridae, Cathartes aura located at the basal position with Haematopus ater. In addition, Pandion haliaetus was clustered with other species of Accipitridae, which was conflict with the traditional classification system by taking P. haliaetus as an independent Familia of Falconidae.