Biodiversity monitoring requires reliable methods for species detection and identification. Here, I examine the use of molecular approaches, including mitochondrial DNA sequencing (barcoding) and environmental DNA (eDNA) analyses in two New Zealand-based case studies. In the first study, I used DNA barcoding to assess the diversity of arthropods collected from the mangroves within RAMSAR protected wetland area in the Firth of Thames, New Zealand. Over one year, a total of 9829 individuals were collected and of these 251 were sequenced. COI sequences were largely congruent with morpho-species designations. The sequences formed 101 putative species, 39% of which contained specimens from outside of New Zealand. 44% of the putative species found at the Thames sites had not been previously found in an inland habitat. I conclude that the terrestrial arthropod community of the mangrove forest in the Firth of Thames is distinctly different from other New Zealand habitats, and may include species not found elsewhere. In the second study, I examined the use environmental DNA (eDNA) as a tool for detecting the presence of New Zealand’s endemic blue duck, or whio, (Hymenolaimus malacorhynchos) in rivers, through water sampling. Species specific primers were designed to target a section of the mitochondrial control region. Water samples were collected from running water within artificial blue duck habitats using an in situ filtration system, eDNA was then extracted from the filter. Any blue duck DNA present in the sample was selectively amplified using the species specific primers. This allowed for blue ducks to be detected through sequencing of the PCR product. In 66% of these cases, it was possible to detect blue duck DNA from the filtered water samples. On this basis, I conclude that there is sufficient “proof of concept” to warrant further investigation into the methods developed here, specifically, the testing of samples from natural environments, in which the presence of H. malacorhynchos has been confirmed by traditional methods.