Diadromy is a life history strategy involving scheduled migrations between freshwater and the ocean. These migrations can maximise fitness across life stages, while also reducing isolation, evolutionary divergence, and speciation rates by maintaining genetic connectivity. However, loss of the marine stage has occurred in many diadromous fish species, causing them to become isolated permanently or semi-permanently in freshwaters. Fish that become landlocked may undergo physiological, morphological, and behavioural changes since they spent at least some parts of their life cycle in a different habitat with differing salinities, diets, parasites, and predators. However, long-term isolation can also enhance genetic diversity among populations and formation of new species. All freshwater fish species in New Zealand are either diadromous or have evolved from a diadromous ancestor. Common smelt, Retropinna retropinna and Stokell’s smelt, Stokellia anisodon are two diadromous fish species native to New Zealand. Common smelt is widespread in New Zealand that can also form landlocked populations, while Stokell’s smelt is limited to several rivers in the Canterbury region. Although landlocking is widespread on Chatham Island, these populations have not been studied in depth, and there is some ongoing taxonomic uncertainty about smelts in New Zealand. In this study, I aimed to understand the phylogeographic structure of smelts throughout New Zealand and their phylogenetic relationship with other retropinnids, the evolutionary history of landlocking on Chatham Island, and the effects of landlocking on morphological and genetic differentiation of common smelt. Overall, this study provides insights into the evolutionary history of smelts and the morphological and genetic effects of landlocking, with implications for the management and conservation of native diadromous fish species in New Zealand.