Pycnogonida, or sea spiders, are an ancient group of arthropods found throughout all the world’s oceans including the Southern Ocean where they have their greatest diversity. Herein we annotate a global mitochondrial dataset containing 197 specimens, including 18 newly sequenced Antarctic species. The presence of novel gene rearrangements, conserved gene overlaps, and the potential for unique mitochondrial genome synapomorphies for specific clades is also investigated. Gene overlaps were common in all families except those in the superfamily Nymphonoidea. The loss of the overlaps in Nymphonoidea may have facilitated the unique gene rearrangement in the group. We confirm Dodecolopoda mawsoni as sister to Decolopoda within Collosendeidae, and Austroraptus juvenilis as a member of Ammotheidae, although its precise affiliation with other genera is unclear due to potential misidentifications in published sequences. We highlight that Pallenopsis spicata requires additional taxonomic attention and we reassign Pentapycnon geayi Bouvier, 1911 to Pycnogonum as Pycnogonum geayi comb. nov. (Bouvier, 1911)and confirm Pentapycnon as endemic to the Southern Ocean. We discuss the placement of Antarctic species with respect to hypotheses on Antarctic origins, but further analyses are required to fully address this question.