The diversity and biogeography of the Antarctic benthos has been shaped by its unique history through glacial cycles, the influence of circumpolar current regimes and seasonal food inputs. There is currently a large international research effort to define levels of species diversity, biogeography, functional traits and their sensitivity to changing environmental conditions. These data are vital in setting ecological baselines to monitor the effects of climate change and manage the impacts of human activities in the Southern Ocean. The findings from genetic level analyses into species diversity, biogeography and the trophic traits of two groups of benthic Antarctic polychaetes, an abundant taxa within macrofaunal communities are presented here. The first group contained free-living polychaetes collected from the Scotia, Amundsen and Weddell Seas, whilst the second group consisted of symbiotic polynoids taken from coral host species in the South Orkney Islands Southern Shelf Marine Protected Area. The application of DNA barcoding to a subset of 15 morphologically identified polychaete species (morphospecies) from the free-living polychaetes, uncovered 10 additional cryptic species (these individuals are morphologically identical but genetically distinct) and 10 previously overlooked morphospecies. These findings suggest that the levels of Antarctic benthic diversity may be largely underestimated. The difficulty in determining true ‘species’ from genetic analysis for which there are no genetic cut offs or rules is discussed, as well as the causes of misidentification of soft bodied species within large sample sets. The distribution of cryptic species are often more restricted that that of their original morphospecies. This is potentially related to geographic or reproductive isolation of populations during the speciation process. In this study, the cryptic species previously considered to be circum-Antarctic remained widespread. This demonstrates the importance of considering dispersal mechanisms, including developmental mode and larval biology and subsequently transport via cicrum-Antarctic currents. The determination of trophic traits using both bulk and compound specific stable isotope analysis, revealed high levels of variability within and between species with the same categorical trophic traits. These data suggest a high degree of omnivory coupled with variation at the base of the food web i.e. in 15N of phytoplankton/phytodetritus. The use of genetic and biochemical analyses to describe the symbiotic relationship between polynoid symbionts and their host corals identified polymorphisms with significantly different trophic signatures. The relevance and significance of the findings are discussed with regard to environmental change in the Southern Ocean and the future of Antarctic marine management and scientific research. Antarctica represents one of the most rapidly changing and vulnerable ecosystems on our planet. Any means to mitigate the effects of climate change or to sustainably manage Antarctic marine resources requires international and multidisciplinary research collaborations. Future research should focus on understanding the interacting and changing relationships between the biological, chemical, physical and geological environments
