Abstract The family Syngnathidae (seahorses, sea dragons and pipefishes) is a fascinating group. Species are mostly distributed in marine coastal waters, but about 30 species inhabit Indo-Pacific tropical island rivers. There are currently six freshwater genera of Nerophinae (trunk-brooders): Belonichthys, Coelonotus, Doryichthys, Lophocampus, Microphis and Oostethus. Unlike other Syngnathidae, freshwater pipefish have been little studied; the taxonomy of Nerophinae is unclear and only based on morphomeristic data. The purpose of our study is to undertake a revision of this group based on an integrative taxonomy approach. By combining molecular data from four mitochondrial markers (5415 bp), morphomeristic data with a character mapping study and ecological data, we now recognize a single genus as valid, Microphis, as opposed to the six previously accepted. Our results also reveal one new candidate species, Microphis nicoleae sp. nov., and the resurrection of two others: Microphis torrentius and Microphis vaillantii. This study shows the relevance of integrative taxonomy for higher taxa delineation, using data integration by congruence.