Colossendeis megalonyx Hoek, 1881 is a widespread and abundant pycnogonid in the Southern Ocean which has also been reported from the South Atlantic and South Pacific Oceans. Its strictly benthic lifestyle is expected to promote genetic differentiation among populations and ultimately facilitate speciation. On the other hand, the reported eurybathy and unknown larval stages of this species may allow Colossendeis megalonyx to maintain genetic continuity between isolated shallow-water habitats by active dispersal through the deep sea or by passive rafting on floating substrates. Thus, it remains unknown whether and to which extent geographically separated populations of Colossendeis megalonyx maintain gene flow in the Southern Ocean. We sampled 96 specimens of Colossendeis megalonyx from three stations in the Atlantic Sector of the Southern Ocean and one station from the South American continental shelf (Burdwood Bank). The genetic structure of nominal Colossendeis megalonyx as well as its phylogenetic position within the genus Colossendeis were assessed using a fragment of the cytochrome c oxidase subunit 1 gene. Our data strongly support that nominal Colossendeis megalonyx consists of at least five cryptic and one pseudocryptic mitochondrial lineages, four of which appear to be geographically restricted. Two lineages occurred at locations separated by more than 1,000 km in the Antarctic, thus indicating high levels of gene flow or recent colonization. No haplotype sharing across the Polar Frontal Zone was observed. Our results strongly suggest that cryptic speciation occurred within the genus Colossendeis. The wide biogeographic distribution range of Colossendeis megalonyx and perhaps that of other Antarctic pycnogonids should therefore be regarded with caution.