Although embryonic development in ascidians has been studied for over a century, the signals involved in coordinating post-larval development and metamorphosis are just beginning to be investigated. In this paper, we demonstrate that transcription is necessary for both the acquisition of metamorphic competence and the completion of the initial events of metamorphosis in Boltenia villosa. Transcripts expressed during metamorphic competence were isolated by a suppressive PCR subtraction of Boltenia villosa larval cDNAs. One of these transcripts is homologous to cornichon. Cornichon has a crucial but undefined role in epidermal growth factor (EGF) signaling during Drosophila embryogenesis. In situ hybridization demonstrates that Boltenia cornichon (Cnib) is expressed in the anterior papillary region of larvae as they gain competence. Our hypothesis is that Cnib acts to potentiate EGF signaling, thereby allowing Boltenia larvae to respond to cues for metamorphosis. Further research into the role of Cnib in urochordate metamorphosis may provide insight into the function of cornichon in other organisms. A better molecular understanding of urochordate metamorphosis will also provide a foundation for exploring the role of metamorphosis in chordate evolution.