The evolution of joints, which afford skeletal mobility, was instrumental in vertebrate success. Here, we explore the molecular genetics and cell biology that govern jaw joint development. Genetic manipulation experiments in zebrafish demonstrate that functional loss, or gain, of the homeobox-containing gene barx1 produces gain, or loss, of joints, respectively. Ectopic joints in barx1 mutant animals are present in every pharyngeal segment, and are associated with disrupted attachment of bone, muscles and teeth. We find that ectopic joints develop at the expense of cartilage. Time-lapse experiments suggest that barx1 controls the skeletal precursor cell choice between differentiating into cartilage versus joint cells. We discovered that barx1 functions in this choice, in part, by regulating the transcription factor hand2. We further show that hand2 feeds back to negatively regulate barx1 expression. We consider the possibility that changes in barx1 function in early vertebrates were among the key innovations fostering the evolution of skeletal joints.