Within the Southern Ocean (SO), the Antarctic Circumpolar Current (ACC) is hypothesized to facilitate a circumpolar distribution for many taxa, even though some, like pycnogonids, are assumed to have limited ability to disperse based on brooding life histories and adult ambulatory capabilities. With a number of contradictions to this circumpolarity reported in the literature for other pycnogonids, alternative hypotheses have been explored, particularly for Nymphon australe, the most common species of Pycnogonida (sea spider) in the SO. Glacial events have been hypothesized to impact the capacity of organisms to colonize suitable areas without ice coverage as refuge and eurybathic capacity to colonize deeper areas. In this study, we examine populations of one presumed circumpolar species, the pycnogonid N. australe, from throughout the Western Antarctic using a 2b-RAD approach to detect genetic variation with Single Nucleotides Polymorphisms (SNPs). Using this approach, our work found that the N. australe included two distinct groups from within the >5000 km sampling region. Using a discriminant analysis of principle components (DAPC), sparse nonnegative matrix factorization (sNMF), and admixture coefficient analysis, two distinctive populations were revealed in the Western Antarctic, with one, covering distances greater than 5,000 km (Weddell, Western Antarctic Peninsula, Ross Sea), while the other group shares limited connectivity entrained within the Amundsen Sea. Under further scrutiny of the 3,086 SNPs, one population had private alleles at 158 SNP loci and the other population had private alleles at 369 SNP loci. We propose the populations analyzed were divergent enough to constitute two different species from within this common Antarctic genus known for its phenotypic plasticity.