The Arctic and the Antarctic harbor major biological resources and the polar oceans are highly productive. Thus, they constitute rich feeding grounds for top predators such as fish, marine mammals or sea birds. The Arctic and Antarctic are characterized by harsh environmental conditions like low temperatures, extreme light regimes or large ice covers. As a consequence they sustain highly distinctive biomes with unique adaptations to these conditions. Which are on the other hand especially vulnerable to the ongoing climate change reflected e.g. by ocean warming, acidification or the decline of the sea ice cover. These consequences are already now apparent in the Arctic and some regions of the Antarctic, where e.g. the surface waters have warmed over the past years (IPCC, 2007a). Furthermore, in the Southern Ocean there is evidence for changes in plankton abundance and community structure. The abundance of Antarctic krill (Eupausia superba), the key component of the diet of whales and other marine mammals has declined in abundance by more than an order of magnitude west of the Antarctic Peninsula during the past 25 years. This observation has been linked to reduced food availability in form of phytoplankton blooms in summer and ice algae in winter  and has major impact on marine vertebrate re-productivity . These studies on consequences of climate change mainly focus on larger plankton organisms. To date there is only little information for the smallest fractions of the ecosystems in these areas. With regard to present changes in the food webs of Polar Regions regular plankton observations that include the smallest fractions should be carried out. This would aid to identify e.g. annually reoccurring patterns at the base of the food webs reflecting stability in Polar Regions. Therefore, PLANKTOSENS aims at mapping the molecular plankton diversity in the Polar Regions and at the development of a molecular based observation strategy that allows for a monitoring of plankton with high spatio temporal resolution.