No other group of animals typifies the uniqueness of Antarctic life more than Pycnogonida (sea spiders), with 20% of all known species found in the Southern Ocean, and 64% of these endemic to the Antarctic. Despite nearly 200 years of research into pycnogonids and other benthic phyla in Antarctica, the parameters which drive the distribution and diversity of benthic fauna are still poorly understood. This study aimed to investigate the diversity and connectivity of pycnogonid communities on either side of the Antarctic Polar Front, with an emphasis on the role of water depth, using an occurrence dataset containing 254 pycnogonid species from 2187 sampling locations. At depths shallower than 1000 m, communities to the north and south of the Antarctic Polar Front were distinct, while below this depth this geographic structure disintegrated. The Polar Front, or the expanse of deep ocean it bisects, seemingly acts as a semipermeable barrier to species exchange between well-sampled shallow communities. The less sampled and less understood deep sea appears to be better connected, with high levels of shared species following the northward flow of Antarctic Bottom Water. The exceptionally high diversity and endemism of Antarctic pycnogonids may reflect an apparent competitive advantage in cold waters which leaves them vulnerable to ongoing ocean warming, with increased competition and predation pressures.