Isolated environments can lead to unique biodiversity; however, endemic taxa are often evolutionarily vulnerable to disturbance. While considered very different, both Antarctica and New Zealand face this challenge. To protect these ecosystems, we must first monitor them to assess whether a change falls within the average flux or is the consequence of disturbance. Monitoring programs should utilise various tools to account for biases and ensure that data accurately represents the ecosystem. The development and integration of new technology for monitoring species can improve the resolution of datasets. One method that is increasingly investigated for ecosystem surveillance is Environmental DNA (eDNA). I suggest eDNA is utilised to monitor both Antarctica and New Zealand's endemic fauna. To assess current Antarctic applications, I reviewed the literature on eDNA. While microbiologists have applied eDNA methods extensively, few papers targeted Antarctic vertebrates. I highlight recent developments in population genetics and portable sequencing technologies and discuss how these methods could apply to Antarctic research. As technology and methods develop, so too will the potential for non-invasive monitoring of polar fauna. I identified Orcas (Orcinus orca) and Weddell seals (Leptonychotes weddellii) as potential target species for future population genetic trials in Antarctica. Thus, my second study investigated Antarctic snow samples as a source of Weddell seal DNA. The snow was collected from a single seal imprint at the Turtle Rock breeding colony in McMurdo Sound. I successfully extracted, amplified and sequenced Weddell seal DNA in seven out of thirty-three snow samples. Though my detection rate was low, to the best of my knowledge, this represents the first time Antarctic vertebrate DNA has been extracted from snow. While all seven sequences fall within the Weddell seal clade on my Neighbour-

Joining tree, the branch lengths suggest a high level of divergence, which could pose challenges for future population genetic applications. I identified that storage time, filter removal and sample size may have impacted our eDNA yield and looked to address this in my final study, primarily through using enclosed Sterivex filter units. I first introduce eDNA surveys in a New Zealand context and highlight the value of eDNA for monitoring a conservation dependent species, the kororā (little blue penguin; Eudyptula minor). I extracted DNA from three sample types, feathers, feather soaked water and tank water from the kororā enclosure at the International Antarctic Centre in Christchurch. While amplification from feather samples was unsuccessful, seven out of nine filter water samples were sequenced, and all eight tank samples. As in the Weddell seal sequences, the kororā eDNA, while clustered with Eudyptula minor, is highly divergent. Likewise, all but two of the sequences aligned with Eudyptula minor (16srRNS), but in two samples, there were several high matches with non-penguin species. Both my Weddell seal and kororā chapters highlight the challenges of developing an eDNA protocol and the need for extensive optimisation and standardisation to draw confident conclusions. However, both studies are promising for future eDNA studies targeting the two species. And with robust protocols, eDNA could be applied to key management concerns in both areas. For example, monitoring the Ross Sea Marine Protected Area (MPA) in Antarctica and contributing to the surveillance of invasive predator species in New Zealand. Thus informing the conservation of unique taxa on both sides of the Southern Ocean.