Despite considerable interest in physiology, evolution and life history of Antarctic marine invertebrates, only a limited number of studies have examined the genetic variability and diversity patterns of these organisms. Moreover, understanding and characterizing patterns of Antarctic biodiversity has taken on a degree of urgency because of potential impacts of global warming. To expand an understanding of the evolutionary history of Antarctic marine invertebrates, the genetic diversity of the crinoid Promachocrinus kerguelensis Carpenter, 1888 was investigated, which is documented to have a circumpolar distribution extending to subantarctic islands. Specimens of P. kerguelensis were collected from the western side of the Antarctic Peninsula, and the subantarctic islands South Georgia, South Sandwich and Bouvetøya Island from 2001 to 2004. P. kerguelensis was previously subject to morphological review that conWrmed the taxonomic recognition of only one species. The wide distribution and reported high dispersal capability for P. kerguelensis predicts one large panmictic population. In contrast, nucleotide sequence data from mitochondrial cytochrome oxidase subunit I and cytochrome b genes, collected herein, reveal distinct genetic structure and cryptic speciation within P. kerguelensis. In the Antarctic Atlantic sector alone, there were at least five “species level” clades. Some of these clades are geographically limited, and most exist in sympatry. The largest and most widespread of these clades was examined to help elucidate connectivity along the subantarctic islands of the Scotia Arc and the Antarctic Peninsula. Within this clade, most genetic diversity was contained within populations, but significant divergences were present between regions (Antarctic Peninsula, South Sandwich Is., South Georgia, Bouvetøya Is.), suggesting a corresponding lack of gene flow. Given that P. “kerguelensis” is a well-studied taxon, the finding of considerable genetic diversity within the Atlantic sector alone suggests that the recognized diversity of Antarctica’s benthic marine life may be underestimated, and will rise dramatically with phylogeographic analyses of putative widespread species.