The phylogeny and classification of the charismatic Syngnathidae (e.g. pipefish, seahorses) has not been comprehensively examined to date. In particular, we assessed morphological hypotheses that previously suggested the three ‘seadragon’ genera (Phycodurus, Phyllopteryx, Haliichthys) do not form a monophyletic group. We used three mitochondrial markers to investigate evolutionary relationships within Syngnathidae, and demonstrated that Phycodurus + Phyllopteryx formed a clade that excluded Haliichthys, indicating the elaborate appendages used for camouflage have evolved independently. A time-calibrated tree revealed the divergence of true seadragons as coincident with other kelp-associated fauna. We found evidence for the resurrection of neglected subfamily names, and recovered Doryrhampinae, Nerophinae, Soleganthinae, Phyllopteryginae, Sygnathoidinae and Haliichthyinae as clades. Even after removing these groups from what is currently recognized as Syngnathinae, we showed that the remaining members of Syngnathinae are not monophyletic. In the light of this information, some conclusions about the diversity of reproductive strategies found within ‘Syngnathinae’ need to be re-examined and further revision of syngnathid classification is needed.