Aoraki denticulata, a widespread mite harvestman endemic to the NW South Island of New Zealand, was postulated to constitute an old lineage with deep genetic history. Expanding on previous studies, we explored its genetic diversity and population structure, phylogeography and diversification patterns. We also examined the systematic implications of such a complex scenario through species delimitation analyses under coalescent-based and barcoding gap discovery methodologies. Our results depict the deep evolutionary history of the A. denticulata lineage, which shows high geographic structure and low genetic connectivity among modern populations. Aoraki denticulata is further subdivided into three lineages: a lineage presently inhabiting the northern region of the Southern Alps (and including the subspecies A. d. major), a second lineage in the north-eastern part of the sampled land, and a third one occupying the south-eastern localities. When using species delimitation methods based on coalescence approaches, large numbers of cryptic species were estimated. Based on morphological and biological evidence, we thus argue that these methods may overestimate species in cases in which genetic divergence is unusually large and discuss the systematic implications of our findings.