Diversity is the foundation of all biological and ecological studies. Globally however, biodiversity is under threat from the varied and cumulative impacts of humans on the environment. It is thus necessary to continually develop tools that are able to assess diversity at the scales now required. DNA barcoding has become an increasingly common approach for species identification as it is efficient and can facilitate high throughput analyses without the routine need of taxonomic experts. This thesis examines the genetic diversity of invertebrate groups from Antarctica and New Zealand to gain an understanding of current baseline levels of variability and to facilitate their use as indicators of environmental change. The juvenile stages of Ephemeroptera (mayflies), Plecoptera (stoneflies) and Trichoptera (caddisflies) (EPT taxa) are key components of aquatic food webs and are frequently used as bioindicators of water quality. However, challenges in identifying juveniles to species levels are one factor limiting their more routine use. New Zealand has over 244 caddisfly species 106 species of stonefly and 50 mayfly species all of which are endemic. Here, my primary aim was to obtain COI sequence coverage for the New Zealand EPT taxa using expertly identified collections of adult specimens. A second aim was to examine levels of sequence diversity within taxa and to test the endemicity of the New Zealand fauna through comparison with international records. Thus far, 225 caddisfly BINs, 48 stonefly and 37 mayfly BINs have been generated. Average intraspecific divergences were between 1.2-1.4% for all three orders while average interspecific distances ranged from 24-32%. The designation of all New Zealand EPT species as endemic was supported with interspecific divergences generally above 13%. These data can facilitate the rapid and accurate assessment of larval specimens and can furthermore be used to facilitate research into the phylogenetic and phylogeographic patterns that have shaped the EPT fauna worldwide. I also examined mitochondrial DNA (COI) sequences for three Antarctic springtail (Collembola) species collected from sites in the vicinity, and to the north of, the Mackay Glacier (77oS) within the Ross Sea region. This area represents a transitional zone between two biogeographic regions (North and South Victoria Land). Here, I assessed levels of genetic variability within and among populations of the three putative springtail species. Each of the three recognised species had multiple highly divergent intraspecific populations (5-11.3% sequence divergence). Based on molecular clock estimates, these divergent lineages were likely to have been isolated for 3-5 million years, a time when the Western Antarctic Ice Sheet (WAIS) was thought to have completely collapsed. Given the current isolation of these genetically distinct populations, any future changes in species’ distributions can be easily tracked through the DNA barcoding of individual springtails across the Mackay Glacier ecotone. Collectively these two studies have established baseline levels of COI diversity for New Zealand and Antarctic invertebrates. Furthermore, they have revealed hidden (cryptic) diversity in both regions and presented opportunities to incorporate DNA barcoding into future studies of New Zealand aquatic and terrestrial Antarctic ecosystems.