Cylix tupareomanaia, new genus and species, is described from three specimens (35.5–55.5 mm SL), collected from rocky reefs at 12–17 m depth from Taitokerau Northland, New Zealand. The new taxon shares morphological synapomorphies with the superficially similar Australian endemic Idiotropiscis and Indo-Pacific Acentronura, including head angled ventrally approximately 25° from the principal body axis, enclosed brood pouch, brood pouch plates, prehensile tail, and absence of caudal fin. Cylix tupareomanaia, new genus and species, however, is distinguishable from all other members of the Syngnathidae by the following combination of bony autapomorphic characters: a cup-like crest present anterodorsally on the supraoccipital; and large conspicuous midventral conical spines on the cleithral symphysis and first trunk ring between the pectoral-fin bases. The new species can be further differentiated by genetic divergence in the mitochondrial COX1 gene from Acentronura breviperula, A. tentaculata, Idiotropiscis australe, and I. lumnitzeri (estimated uncorrected p-distances of 19.5%, 20.4%, 17.9%, and 18.4%, respectively). A phylogenetic hypothesis from the analysis of two nuclear loci, 18S and TMO-4C4, supports the placement of C. tupareomanaia, new genus and species, as the sister taxon to a clade comprising the genera Acentronura and Idiotropiscis. Cylix tupareomanaia, new genus and species, represents the eighth member within the pygmy pipehorse clade to be described from the Indo-Pacific and the first new genus and species of syngnathid to be reported from New Zealand since 1921.