AbstractThe development and homologies of the median elements of the ventral hyoid and branchial arches of Cypriniformes have been unclear. We compared the developmental morphology of this region across five species (Cycleptus elongatus, Luxilus zonatus, Danio rerio, Devario auropurpureus, and Cobitis striata), representing three of five major clades of cypriniforms. The development of basibranchial 1 is similar in catostomids and cyprinids, where a single, elongate, basihyal + anterior copula divides into separate elements. A gap develops between the posterior end of the basihyal cartilage and the anterior copula in catostomids but in cyprinids (Luxiluszonatus, Danio rerio, and Devarioauropurpureus) there is little separation and the basihyal and basibranchial 1 may grow close together or retain a cartilaginous connection (Danio rerio, several outgroups). In loaches and Gyrinocheilus, the gap posterior to the basihyal has been alternately interpreted as either the absence or posterior displacement of basibranchial 1. Uniquely among examined species, in Cobitis striata, the basihyal cartilage and anterior copula form as separate cartilages and remain distinct throughout development with a prominent gap between the basihyal and most anterior basibranchial, which we interpret as loss of basibranchial 1. In the posterior region associated with branchial arches 4 and 5, all examined species except Danio rerio, which has only a basibranchial 4 cartilage, have separate basibranchial 4 and 5 cartilages in early ontogeny. Basibranchials 4 and 5 remain separate in Cycleptus elongatus, Devario auropurpurea, and Cobitis striata, but fuse in Luxilus zonatus to form a posterior copula. The orientation of basibranchial 4 and 5 cartilages in Cobitis striata is similar to catostomids and cyprinids. The most posterior median element in the branchial arches, the post‐ceratobranchial cartilage, generally forms as a separate cartilage in catostomids but in Cobitis striata is connected with basibranchial 5 cartilage from earliest appearance. J. Morphol., 2012. © 2012 Wiley Periodicals, Inc.