Seadragons are widely recognized for their derived and novel traits. Research and conservation efforts involving these unique fish species and their relatives have been hindered by a lack of genomic resources. Here we present full, annotated genomes of leafy and weedy seadragons, which help uncover surprising features of gene family and genome architecture evolution that likely relate to extreme phenotypic traits in seadragons, pipefishes, and seahorses. These genomes are important research resources for the Syngnathidae, a diverse, morphologically exceptional group of vertebrates, and for comparative genomic study of vertebrates in general.