The hyomandibular (HM) cartilage securing the lower jaw to the neurocranium in fish is a craniofacial skeletal element whose shape and function have changed dramatically in vertebrate evolution, yet the genetic mechanisms shaping this cartilage are less understood. Using mutants and rescue experiments in zebrafish, we reveal a previously unappreciated role of Pax1a in the anterior HM plate formation through EphrinB2a. During craniofacial development,