Mountains and islands are both model systems for studying the biogeography of diversification and population fragmentation. Aotearoa is an excellent location to study both phenomena due to alpine emergence and oceanic separation. While it would be expected that separation across Te Moana o Raukawa and elevation gradients are major barriers to gene flow in aquatic insects, such hypotheses have not been thoroughly explored in these taxa. Here, we show that mountains and oceanic separation function as semi-permeable barriers for Kapokapowai dragonflies. We show that, although Te Moana o Raukawa, is likely responsible for some of the genetic structure observed, speciation has not yet occurred in populations separated by the strait. Although there is no evidence that they are an impervious barrier, Kā Tiritiri-o-te-Moana do represent a major barrier to gene flow between named species. The distribution of alpine Kapokapowai can also not be explained by the ancestral populations simply rising with the uplifted tectonic plates. Although further research is needed, our findings suggest that the ancestral Kapokapowai colonized alpine habitats after their formation, and then radiated back out to lowlands. These findings suggest that aquatic insects could be an exciting new frontier in the study of the biogeography of Aotearoa.