The diversity of New Zealand’s freshwater copepods has been largely understudied. In order to enhance our understanding of this taxon, I used the mitochondrial cytochrome c oxidase subunit one (COI) gene sequences to examine the diversity of two orders of New Zealand’s freshwater copepods; Cyclopoida and Harpacticoida. Where possible, I also assessed the global affinities of taxa using available sequences from global databases (e.g. GenBank, BOLD). Specimens were collected from several sites across both the North Island and South Island of New Zealand. From these, DNA was extracted from 246 individuals, of which COI sequences were successfully obtained from 84 (a success rate of 34%). Sequences represented 17 species of freshwater copepod; nine species of cyclopoid and eight species of harpacticoid; all species were clearly delineated by the COI gene. Intraspecific sequence divergences were generally <1% whereas interspecific divergences usually exceeded 13%. For the cyclopoid copepods, three taxa (two distinct species of Eucyclops cf. ‘serrulatus’ and Acanthocyclops americanus) showed close molecular affinities to Northern Hemisphere populations (<1% divergent in all cases); and are likely to represent recent human-mediated introductions to New Zealand. Additionally, Mesocyclops ‘leuckarti’ was <1% divergent to an undescribed cyclopoid species from South Australia, likely Mesocyclops australiensis. For the harpacticoids, specimens of Elaphoidella bidens and two geographically distinct populations of Bryocamptus pygmaeus showed high levels of intraspecific diversity (>12% and >18% divergent respectively), suggesting the presence of cryptic taxa. These results suggest that the diversity of New Zealand’s freshwater cyclopoid and harpacticoid copepods is underestimated and several non-indigenous taxa may be present among the New Zealand copepod fauna. I conclude that the COI gene will be a useful tool in assessing New Zealand’s native copepod biodiversity and also in identifying invasive species.