Dispersal of aquatic insects is a key process allowing colonization of new habitat and linking existing populations among habitats. Studying the dispersal of freshwater taxa directly is logistically challenging and assessments of population genetic structure using DNA sequence fragments have provided an alternative means to examine the dispersal and connectivity of natural populations. Here, I used mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences to assess the genetic similarity for aquatic insect species across both small (<50km) and large (>1000km) spatial scales. For the first study, I examined genetic similarity among source and restored stream habitats in Taranaki Region, New Zealand. Three common species were targeted based on differences in dispersal capabilities: Archichauliodes diversus (Megaloptera; active larvae, weak flight), and Hydropsyche colonica and Pycnocentrodes aeris (Trichoptera; sessile larvae, strong flight). Archichauliodes diversus showed the greatest sequence diversity (19 haplotypes) followed by P. aeris (14 haplotypes) and H. colonica (4 haplotypes). Despite relatively high levels of genetic diversity, A. diversus was genetically similar throughout the study area, suggesting adequate dispersal among source and restored habitats. Individuals of H. colonica, with much lower levels of haplotype diversity, were also genetically similar between source and restored habitats. In contrast, P. aeris had one haplotype that was more common in source versus restored habitats. I concluded that taxa were relatively well connected between source and restored habitats and that COI sequences can provide a useful indicator for tracking restoration efforts within relatively small geographic areas. In the second study, I focused on large-scale patterns of diversity for A. diversus which is widespread throughout both the North and the South Islands of New Zealand and compared this with available sequences from a congeneric Australian species. I found sequence divergences between the New Zealand A. diversus and Australian Archichauliodes sp (11.8% divergence), and between New Zealand North Island and South Island A. diversus (3% divergence). In the South Island, there were 8 haplotypes restricted to individual sites and 4 haplotypes that were shared among sites. For the North Island, individuals there were 21 haplotypes restricted to one of more sites and 1 common haplotype shared among Taranaki sites. There were 12 missing mutational steps between haplotypes from the North Island and the South Islands. The Australian Archichauliodes sp was further separated by 70 missing mutational steps from the South Island of New Zealand. Differentiation was also observed within the South Island with shared haplotypes observed at distances of > 150 km. On this basis, I suggested that despite potentially weak flight, individuals of A. diversus can regularly disperse distances of up to 150 km. However, they also appear limited by geographic barriers such as the Cook Strait between the North and South Islands (<25 km). Molecular clock estimates between New Zealand and Australian Archichauliodes sp. suggested that isolation of individuals occurred around 5 Mya and isolation between the North and South A. diversus occurred within the last 2 Mya; corresponding with the Pliocene and Pleistocene, respectively. On the basis of both studies, I concluded that COI gene sequences can provide a useful method for assessing the genetic similarity of aquatic insect populations on both small (<50km) and large (>1000km) spatial scales and that these data can then be used to test ecological and evolutionary hypotheses.