Neopurcellia salmoni is a mite harvestman found throughout the forests of the west coast of New Zealand’s South Island. This species range is unusually large for the notoriously dispersal-limited Cyphophthalmi, raising the possibility of multiple cryptic species within the lineage. In order to test this hypothesis, we used scanning electron microscopy to examine a large number of individuals from throughout its range, and discovered two distinct male morphotypes distinguished by the presence or absence of dorsal glandular pores. We performed phylogeographic and population genetic analyses using DNA sequence data from the fast-evolving mitochondrial locus COI. Tree topologies revealed two well-supported clades within Neopurcellia occupying non-overlapping geographical regions of the west coast. The strong correlation between the evolutionary relationships of lineages within Neopurcellia and the geographic distribution of its populations indicates isolation by distance, as expected with dispersal-limited organisms; population genetic analyses confirm strong isolation of populations. However, we discovered that the distribution of male morphotypes does not follow any geographic or phylogenetic pattern. While the presence of two different morphotypes initially suggested multiple Neopurcellia species, phylogeographic analysis allowed us to reject this hypothesis. We therefore report here the first known case of male polymorphism in the suborder Cyphophthalmi.