The lesser-spotted dogfish (Scyliorhinus canicula) and the North American paddlefish (Polyodon spathula) are two emerging model systems for the study of vertebrate craniofacial development. Notably, both of these taxa have retained plesiomorphic aspects of pharyngeal endoskeletal organization, relative to more commonly used models of vertebrate craniofacial development (e.g. zebrafish, chick and mouse), and are therefore well suited to inform the pharyngeal endoskeletal patterning mechanisms that functioned in the last common ancestor of jawed vertebrates. Here, we present a histological overview of the condensation and chondrogenesis of the most prominent endoskeletal elements of the jaw, hyoid and gill arches – the palatoquadrate/Meckel’s cartilage, the hyomandibula/ceratohyal, and the epi-/ceratobranchial cartilages, respectively – in embryonic series of S. canicula and P. spathula. Our observations provide a provisional timeline and anatomical framework for further molecular developmental and functional investigations of pharyngeal endoskeletal differentiation and patterning in these phylogenetically informative taxa.