There are currently five recognised species of kiwi (Apteryx spp.), and possibly 11 distinct genetic lineages, all of which are threatened or near threatened. Currently, with only approximately 400 individuals left, the most endangered provenance is Haast tokoeka (Apteryx australis ‘Haast’), classified as ‘Nationally Critical’ (Robertson et al. 2017 in Conservation status of New Zealand birds, 2016. New Zealand Threat Classification Series 19. Department of Conservation, Wellington). Several decades ago, a population of tokoeka from the Upper Arawhata region of the Olivine ranges near Haast, New Zealand was discovered, separated from the Lower Arawhata population by the Arawhata River and up to 20 km distance. Here, we used 1283 basepairs from two mitochondrial loci (control region and cytochrome b) and 14 nuclear microsatellites to describe the genetic diversity of this discrete population. Compared to Lower Arawhata, mitochondrial diversity was greater in Upper Arawhata with three mtDNA haplotypes compared to two, despite a lower sample size, and a pairwise nucleotide diversity more than five times as high (π = 0.00082). No mtDNA haplotypes were shared between the two regions. Microsatellites revealed moderate inbreeding in Upper Arawhata (FIS = 0.102), lower diversity levels to Lower Arawhata, and indicated this population is closest to but distinct from Lower Arawhata tokoeka when compared to other recognised tokoeka provenances. The marker-specific disparity in diversity measurements in Upper Arawhata may reflect relatedness in the presence of female dispersal. The low mitochondrial diversity in Lower Arawhata may indicate an over-use of productive females in supplementation programs. The distribution of genetic variation across all tokoeka was consistent with an isolation-by-distance model, but this correlation may be disrupted by local and complete barriers to gene flow creating highly structured regional populations. In summary, we provide strong support for the classification of the Upper Arawhata tokoeka as a genetically distinct population, increasing the genetic variation within Haast tokoeka and providing a useful resource for on-going conservation management.