To investigate jaw evolution in beloniform fishes, we reconstructed the phylogeny of 54 species using fragments of two nuclear (RAG2 and Tmo-4C4) and two mitochondrial (cytochrome b and 16S rRNA) genes. Our total molecular evidence topology refutes the monophyly of needlefishes (Belonidae) and halfbeaks (Hemiramphidae), but supports the monophyly of flyingfishes (Exocoetidae) and sauries (Scomberesocidae). Flyingfishes are nested within halfbeaks, and sauries are nested within needlefishes. Optimization of jaw characters on the tree reveals a diverse array of evolutionary changes in ontogeny. During their development, needlefishes pass through a “halfbeak” stage that closely resembles the adult condition in the hemiramphid halfbeaks. The reconstruction of jaw transitions falsifies the hypothesis that halfbeaks are paedomorphic derivatives of needlefishes. Instead, halfbeaks make up a basal paraphyletic grade within beloniforms, and the needlefish jaw morphology is relatively derived. The parallel between needlefish ontogeny and beloniform phylogeny is discussed, and clades amenable to future morphological analysis are proposed.