To build complex organs, embryos have evolved mechanisms that integrate the development of cells unrelated to one another by cell type or ancestry. Here we show that the pha-4 locus establishes organ identity for the Caenorhabditis elegans pharynx. In pha-4 mutants, pharyngeal cells are transformed into ectoderm. Conversely, ectopic pha-4 expression produces excess pharyngeal cells. pha-4 encodes an HNF-3 homolog selectively expressed in the nascent digestive tract, including all pharynx precursors at the time they are restricted to a pharyngeal fate. We suggest that pha-4 is a key component of a transcription-based mechanism to endow cells with pharyngeal organ identity.