Seagrasses are a unique marine ecosystem that form extensive beds throughout coastal, estuarine areas and harbour rich and diverse taxonomic groups. Throughout the globe, seagrasses have experienced decline and there is a growing need to understand how patterns in biodiversity and distribution respond to increasing stressor. In New Zealand, seagrass ecosystems consist of one species (Zostera mulleri), however, the biodiversity value of these habitats remains understudied. To asses spatial and temporal variation, seagrass associated faunal communities were sampled in 9 locations across New Zealand. One of these locations (Duvauchelle bay) was sampled over the span the year to gain understanding how Z. muelleri systems may vary naturally over the seasons. This study exemplifies the highly variable nature of seagrass systems as regions and sites differed in overall species composition and abundance. Southern sites were found to support the most diverse communities, whereas, northern sites supported the most abundant communities. Results suggest that sites that are either in close proximity of large-scale development will experience reductions in their taxonomic communities. Furthermore, surrounding landscape and topography were attributed to changes seen across sites. Only isolated sites supported populations of pipefish, suggesting that pipefish may be useful ecological indicators for Z. muelleri systems in New Zealand.