ABSTRACT We describe two new species in the genus Gobiomorphus, a radiation of fresh and brackish water gudgeons known from Australia and New Zealand. These species are a prominent component of New Zealand’s freshwater ichthyofauna and most are widely distributed throughout both the North and South Islands. Two of the inland species, G. breviceps and G. basalis, are composed of disjunct northern and southern populations that are distinguishable with molecular data. We examine individuals from across the ranges of both species, identify morphological differences between them, and describe two new species: Gobiomorphus dinae n. sp. (distinct from G. basalis) and Gobiomorphus mataraerore n. sp. (distinct from G. breviceps). Although the species are similar, they vary in dorsal spine count (G. dinae) and pectoral fin ray count (G. mataraerore). We provide mitochondrial COI sequences for each species pair to facilitate identifications by DNA barcoding. These species represent examples of divergence in allopatry, with diagnostic characters arising over the last 2−5 million years in the G. breviceps/G. mataraerore pair, and fewer than 2 million years in the G. basalis/G. dinae pair. We also designate a lectotype for G. basalis (the paralectotype is G. cotidianus) in order to clarify confusion surrounding the original syntypes.