Gnathostome vertebrates have multiple members of the Dix family of transcription factors that are expressed during the development of several tissues considered to be vertebrate synapomorphies. including the forebrain, cranial neural crest, placodes, and pharyngeal arches. The Dix gene family thus presents an ideal system in which to examine the relationship between gene duplication and morphological innovation during vertebrate evolution. Toward this end, we have cloned Dix genes from the lamprey Petromyzon marines, an agnathan vertebrate that occupies a critical phylogenetic position between cephalochordates and gnathostomes. We have identified four Dix genes in P. marines, whose orthology with gnathostome Dir genes provides a model for how this gene family evolved in the vertebrate lineage. Differential expression of these lamprey Dix genes in the forebrain, cranial neural crest, pharyngeal arches, and sensory placodes of lamprey embryos provides insight into the developmental evolution of these structures as well as a model of regulatory evolution after Dix gene duplication events.