Key innovations, traits that provide species access to novel niches, are thought to be a major generator of biodiversity. One commonly cited example of key innovation is pharyngognathy, a set of modifications to the pharyngeal jaws found in some highly species rich fish clades such as cichlids and wrasses. We sequenced and assembled genomes of previously unsequenced pharyngognaths and close relatives to examine the evolutionary history of transitions to pharyngognathy as well as its comparative genomic basis.