The population genetic of the Antarctic benthic shrimp Notocrangon antarcticus was analyzed with 3 polymorphic microsatellite markers and with the 16S rDNA gene. Therefore, samples from 7 different locations: Antarctic Peninsula (Larsen A, Larsen B and Larsen C), South Orkney Island, South Georgia Island, East Weddell Sea and Terre Adélie were collected during the CEAMARC (2007) and CAMBIO (2011) expedition. The results of the mitochondrial 16S gene marker showed two clades within the haplotype network, one for South Georgian samples and the other one for the rest of the samples tested herein (Antarctic Peninsula, South Orkney Island, East Weddell Sea and Terre Adélie). The microsatellite data reinforced the results from the 16S haplotype network showing as well genetically differentiated population clusters – one for SGI and one for the rest of specimen of the continental shelf and the South Orkney Island (SOI). In addition, the microsatellite data gave some hints on a further genetically partially differentiated population for the samples of the Larsen C shelf of the Antarctic Peninsula. Last mentioned however, still needs to be further analyzed. All in all, the population of SGI shows a clear genetic isolation from all other tested populations and can be considered as an independent evolutionary significant unit (ESU). Furthermore N. antarcticus seems to have a circumpolar distribution with more or less constant gene flow around the Antarctic continental shelf including the island of South Orkney. Nevertheless, further microsatellite primers should be isolated in order to give higher evidence to the data. Usually, six to eight polymorphic markers are recommended for such tests. In addition, the number of individuals tested per location should also be increased.