Pharyngeal arches are paired columns of tissue that form when pouches of foregut endoderm contact surface ectoderm on either side of the embryonic vertebrate head. In fishes, endodermal pouches fuse with surface ectoderm to form gill slits. Once delineated, pharyngeal arches undergo morphogenesis and differentiation, giving rise to skeletal elements of the jaw and gills (in fishes), or the jaw, ear and throat (in amniotes). In my first data chapter, I demonstrate a requirement for Fgf signalling in endoderm–ectoderm fusion and gill slit formation in a cartilaginous fish, the little skate (Leucoraja erinacea). Once formed, skate gill arches expand laterally, and give rise to cartilaginous appendages called branchial rays, which develop under the influence of a Shh-expressing signalling centre called the gill arch epithelial ridge (GAER), and arise exclusively within the posterior region of the gill arches. In my second data chapter, I demonstrate that the skate GAER is of endodermal origin, forming at the endoderm–ectoderm interface, and I discover that Wnt signalling from GAER-adjacent ectoderm contributes to the maintenance of gill arch anteroposterior skeletal polarity, by restricting GAER Shh signal transduction and chondrogenesis to the posterior arch environment. Chick (Gallus gallus) embryos also have a SHH-expressing signalling centre (the posterior ectodermal margin, or PEM) in their second (hyoid) pharyngeal arch, which is associated with posterior expansion of the hyoid arch and neck closure. In my final data chapter, I show that an initially broad domain of SHH expression in the posterior hyoid arch epithelium splits into two discrete domains – the PEM and a domain in the proximal hyoid epithelium (PHE) – with distinct functions in promoting hyoid arch expansion and middle ear skeletogenesis, respectively. Taken together, my work reveals molecular mechanisms important for the formation and patterning of pharyngeal arches and the pharyngeal skeleton across jawed vertebrates.