The phylogeny of the tribe Aquilini (eagles with fully feathered tarsi) was investigated using 4.2 kb of DNA sequence of one mitochondrial (cyt b) and three nuclear loci (RAG-1 coding region, LDH intron 3, and adenylate-kinase intron 5). Phylogenetic signal was highly congruent and complementary between mtDNA and nuclear genes. In addition to single-nucleotide variation, shared deletions in nuclear introns supported one basal and two peripheral clades within the Aquilini. Monophyly of the Aquilini relative to other birds of prey was confirmed. However, all polytypic genera within the tribe, Spizaetus, Aquila, Hieraaetus, turned out to be non-monophyletic. Old World Spizaetus and Stephanoaetus together appear to be the sister group of the rest of the Aquilini. Spizastur melanoleucus and Oroaetus isidori are nested among the New World Spizaetus species and should be merged with that genus. The Old World 'Spizaetus' species should be assigned to the genus Nisaetus (Hodgson, 1836). The sister species of the two spotted eagles (Aquila clanga and Aquila pomarina) is the African Long-crested Eagle (Lophaetus occipitalis). Hieraaetus fasciatus/spilogaster are closest to Aquila verreauxii and should be merged with that genus. Wahlberg's Eagle H. wahlbergi, formerly placed in Aquila, is part of a clade including three small Hieraaetus species (pennatus, ayresii, and morphnoides). The Martial Eagle (Polemaetus bellicosus) is the sister species of the Aquila/Hieraaetus/Lophaetus clade. Basal relationships within this clade remained unresolved. Parsimony reconstruction of the evolution of plumage pattern within Aquilini suggests that: (1) transverse barring of parts of the body plumage was lost in the Palearctic Aquila-Hieraaetus clade, (2) pale underparts in adult plumage evolved three times independently, and (3) dimorphic adult plumage is a derived character of the small-bodied Hieraaetus clade.