The ability to accurately monitor biological diversity is the foundation to most ecological research. However, the morphological identification of spiders, as with many arthropod taxa, is often complicated by phenotypic plasticity and sexual dimorphism. New Zealand’s spider fauna is highly endemic (97% of known species), consisting of an estimated 2,000 species. Given such high diversity, it is critical to seek cost-effective measures of assessing species diversity and distributions, and for the identification of cryptic unidentified taxa. The aim of my research was to determine whether the described spider fauna can be effectively delineated from unidentified taxa using DNA barcoding. Overall, I establish a molecular inventory for 100 described species and 71 additional unidentified species of spiders found in New Zealand. Using barcoding I determined there to be 59 native described species and classify 66 of the unidentified species as native, leaving 45 species which were recognised as having international distributions by taxonomic descriptions and/or from comparative DNA sequences from the Barcode of Life Datasystem (www.boldsystems.org). The repository of species presented here represent native species pertaining to 26 families and cosmopolitan species from 17 families of which species from the Araneidae, Linyphiidae and Theridiidae families are the most diversly represented in this study. This foundational inventory was used to assess the presence of spider species around the marginal habitats of 5 Waikato study lakes (Puketi, Rotoiti, Kohahuake, Waiwhakareke and Koraha), in relation to community assemblage variation across lakes, habitat (shoreline vs. pasture) and sampling method. The combined morphological and molecular approach to identification used here has demonstrated community composition assessments of spiders are viable. Furthermore, the study of these community assemblages revealed a greater diversity of habitat specialists among shoreline samples from lakes Kohahuake, Koraha and Waiwhakareke where greater vegetative heterogeneity along the shoreline provides a greater range of niches for spiders to occupy. This compiled species inventory indicates that New Zealand’s diverse Araneae fauna has been infiltrated by species with international distributions. Further, not all species are easily recognisable due to dissimilarities in their morphological appearance, or because they remain to be genetically identified, and therefore the extent of non-native species infiltration into New Zealand ecosystems is unclear. This lack of knowledge highlights an important area for future biosurveillance work. Lake ecosystems were selected for this study because a variety of spider species prey upon adult aquatic invertebrates as they emerge from the aquatic realm and into the terrestrial. Methods which provide complementary data for ranking lake ecosystems is a priority for biodiversity management in the Waikato region due to habitat fragmentation primarily associated with deforestation and subsequent conversion to pastoral habitat. Land use practices affect the distribution and dispersal of many native species and connected expanses of pasture provide opportunities for exotic species to infiltrate established food-webs associated with ecosystems of significant natural character. In conclusion, this molecular inventory provides a key foundation for a COI barcode library for New Zealand’s most commonly-encountered spiders and validates the ability of this identification method to discern between male, female and juvenile specimen from described and unrecognised species with native or international distributions.