Early vertebrate genome evolution has long been in need of clarification, and it is now of particular interest because several distantly related vertebrate genomes have been recently sequenced. We reconstructed the gnathostome (jawed vertebrate), osteichthyan (bony vertebrate), and amniote (the group including reptiles, birds, dinosaurs, and mammals) ancestor genomes, which are located at key phylogenetic positions, leading to a novel scenario of genome evolution in early vertebrates.