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The Antarctic benthos is rich in biodiversity, with many species being endemic to the Southern Ocean. Multiple factors such as oceanic currents, glacial cycles and reproductive life stages have been attributed to the distribution of benthic dwelling invertebrates around the continent. The sea spider (Pycnogonida) Nymphon australe is a paternal brooder, which lacks a pelagic planktonic life stage. Typically brooding is assumed to suggest limited dispersal capabilities. Here we investigated the genetic structure of N. australe, a highly abundant pycnogonid species in the Southern Ocean to test assumptions of a documented circumpolar distribution. Previous studies with mitochondrial data have revealed that N. australe has high genetic diversity, limited gene flow, as well as distinct geographic structure. To resolve the phylogeographic structure of the circumpolar N. australe from the Antarctic continental shelf, we used 3RAD single nucleotide polymorphism (SNP) data from 111 individuals sampled from ten different, circumpolar geographic regions including the Western Antarctic Peninsula, Ross Sea, Weddell Sea, and Eastern Antarctica. Analyses revealed populations to have distinct regional populations with strong geographic structuring observed by locality and suggest the possibility that N. australe may be a species complex in the Southern Ocean.