The Arctic Ocean is a threatened environment and climate change is expected to be particularly intense by having extensive consequences on the pelagic ecosystem. Hence, evaluations of the impact on the base of the food web, on local phytoplankton communities, are required. Prerequisite of such an evaluation is comprehensive information about the present phytoplankton diversity and distribution. Recent investigations indicate that rising temperatures as well as freshening of surface waters in the marine environment promote a shift towards picoeukaryotes. In such a scenario, picoplankton can comprise a large pool of biomass by attaining high abundances. Understanding the impact of climate related environmental change for this phytoplankton size class in the Arctic Ocean demands that we understand how environmental variables influence their diversity, occurrence and distribution. In this perspective sampling has take place in the central Arctic Ocean, the Laptev Sea and the Fram Strait to obtain divers hydrodynamic conditions. Thereby, special focus is set on sampling the latter area since it implies a frontal zone separating water masses originating from the WSC (West Spitsbergen Current) and EGC (East Greenland Current) and constitutes the main water exchange into the Arctic Ocean. Consequently anticipated intrusions of invasive species into the polar habitat are likely to be first reported in this region why it is regularly sampled on annual basis (2009, 2010 and 2011). The analysis has been carried out by the application of ribosomal fingerprinting technology (ARISA) to assess the community structure and of Next Generation Sequencing to analyze the diversity assessment. Preliminary results on the investigation of the genetic diversity reflect the environmental differences by presenting different community structures according to the water masses. Further the findings reveal a comparatively higher diversity within the warm water masses. By keeping the track of the Atlantic Water the dominance of single species like Phaeocystis pouchetii attracts attention wherein the influences of the Kongsfjord fortunate more tolerable species like Micromonas pusilla. The community structure of the EGC by contrast displays a distinct community structure and point to a different diversity within the current. So far picoplankton can have a high share of total protist biomass in aquatic systems, so that changes in their diversity or abundance are likely to affect prospectively pelagic food web systems up to higher trophic levels. Our results indicate the necessity of considering ocean hydrodynamics in the course of investigations and assessments of the distribution and diversity of picoeukaryotes. Altogether, this study shall deliver a framework for better understanding the interactions between environmental conditions and corresponding picophytoplankton communities by assessing the presence of biogeographic patterns.