Biofouling pests, including non-indigenous species, can have significant impacts on anthropogenic activities. This is particularly true for aquaculture industries, where biofouling communities grow on crop species and infrastructure, potentially reducing revenue and increasing processing and production costs. It is of interest to marine farmers and scientists to gain a better understanding of the processes facilitating the regional proliferation and spread of biofouling pests. The structure of biofouling communities associated with marine farms in New Zealand’s main mussel growing region, Pelorus Sound, are characterised in this thesis. The patterns of connectivity and gene flow among biofouling populations are also investigated. Images and video footage of biofouling on mussel farms (Perna canaliculus) indicate strong spatial variation in the structure of biofouling communities, with a dominance of known problematic taxa and high wave energy tolerant species, such as the brown alga Undaria pinnatifida and the calcareous tubeworm Pomatoceros sp., near the entrance of Pelorus Sound. Genetic analyses and simple GIS-based modelling of a case study biofouling organism, Didemnum vexillum, revealed genetic differentiation among populations with extreme outcrossing and low levels of connectivity. Genetic analyses also suggest that anthropogenic-assisted dispersal may be vital for connecting certain D. vexillum populations compared to natural spread. The present study illustrates how multidisciplinary research approaches can be used to identify geographical areas that are less prone to biofouling and to inform the management of biofouling pests and invasive species in aquaculture environments.