Increasing anthropogenic habitat fragmentation in riverine ecosystems, in particular the loss of natural riparian vegetation, has profound consequences for dispersal and connectivity of aquatic insects. Aquatic insects depend on dispersal to colonise new sites and expand their ranges, but colonisation is only effective if followed by successful reproduction of the colonising individual within the receiving population. Populations that are connected by dispersal are likely to possess and maintain higher levels of genetic diversity through gene flow, which enhances their long-term viability. Conversely, altered and/or restricted movement of individuals in fragmented landscapes may disrupt the connectivity of populations across habitats, reducing gene flow and decreasing genetic diversity of remnant populations. Thus, the ability to successfully disperse through fragmented and disturbed patches can be a key determinant of the long-term viability of populations. Genetic markers provide an indirect approach to estimate dispersal potential and infer a species’ gene flow, genetic diversity, and population connectivity. A variety of different genetic markers have been used over the past decades, each with advantages and disadvantages. Mitochondrial DNA (mtDNA) is commonly used in aquatic insect research and provides insight into historic dispersal, connectivity and isolation, while nuclear markers identified through next-generation sequencing approaches can reflect changes on a more contemporary time scale. The application of such markers in landscape genetics research further enables quantification of the effects of landscape and environmental features on gene flow, and identification of potential barriers to dispersal. This thesis is a collection of individual research papers that together provide new knowledge of functional connectivity and dispersal patterns of stream insect populations in altered landscapes. The research findings could ultimately assist with conservation and restoration planning. An overview of the most commonly-used genetic markers, including their main features as applied to studies of aquatic insect dispersal, is provided as a global review in Chapter 2. Traditional markers, such as allozymes and mtDNA, are the most popularly applied and studies assessing the effects of specific landscape features on shaping population connectivity among habitats, especially in fragmented landscapes, are rare. Higher resolution markers (e.g. single nucleotide polymorphisms; SNPs), have recently become available, providing high- throughput genome-wide data at low cost. With their potential to detect finer-scale genetic structure, these markers are expected to become more common in future studies, providing more accurate estimates of contemporary patterns of dispersal. Chapter 3 compares the resolution power of mitochondrial cytochrome c oxidase subunit I (COI) and genome-wide SNP markers in estimating fine-scale genetic differentiation for three endemic New Zealand aquatic insects. Both markers provided comparable results: a general lack of strong population structure within each species, and fine-scale genetic differentiation among some populations. These results indicated substantial connectivity of the three analysed species within and between proximate streams separated up to 11 km. However, findings were considered preliminary as small sample sizes and limited data quality for the SNP datasets may have compromised their power to uncover genetic structuring. Nevertheless, an important overall finding was that either COI or SNP markers can provide suitable initial estimates of fine-scale population genetic differentiation in stream insects. Finally, Chapter 4 provides a detailed analysis of functional connectivity and dispersal patterns for the three stream insect species at multiple spatial scales, increasing the sample size and geographic coverage of sequenced individuals from Chapter 3. For all three species, clear spatial genetic structure marked by Isolation by Distance (IBD) was only observed at larger spatial scales (among mountain regions separated by ~30 and 170 km), whereas most gene flow occurred locally (up to 11 km). At the local spatial scale, landscape genetic analyses revealed that Isolation by Resistance (IBR) - particularly the influence of land cover - generally provided a better prediction of spatial genetic structure. Species-specific findings further highlighted the potential influence of continuous forest in the riparian zone in enhancing population connectivity and dispersal within the stream channel. Meanwhile, dispersal over pastoral land may be more common when insects must search for suitable habitat that cannot be found locally. These key findings are likely to be fundamental for future colonisation and persistence of these populations. Understanding in-stream and overland dispersal, and how these affect the gene flow of species, is important for successful implementation of stream restoration measures. This research collectively elucidated patterns of population connectivity and dispersal potential in a fragmented landscape that will provide valuable knowledge for conservation efforts aimed at enhancing restoration of stream insect biodiversity.