Climate change is expected to be particularly intense in the Arctic Ocean having as well extensive consequences on Arctic pelagic ecosystems. Thus, 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 in the phytoplankton community towards a dominance of smaller cells. In such a scenario, picoplankton can comprise a large pool of biomass and can attain 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 parameters influence their diversity, occurrence and distribution. In this perspective, samples to investigate picoplankton have been taken in the area of the “deep-sea long-term observatory HAUSGARTEN” of the Alfred-Wegener-Institute (Fram Strait) in July 2009 and analyzed by the application of ribosomal fingerprinting technology (ARISA), 18S rDNA clone libraries and Pyrosequencing. The investigation area between 2 - 6°E and 78 – 80°N is located within the frontal zone which is separating the warm and cold water masses originating from the West Spitzbergen Current and East Greenland Current, respectively. Based on the heterogeneous hydrographic condition differences in the picoplankton community according to the water masses is likely. Preliminary results on the investigation of the genetic diversity of picoplankton reflect these environmental differences. The findings reveal that the diversity within the warm water mass is higher compared to the one found in the colder water mass. Further the dominance of single species (Phaeocystis pouchetii vs. Micromonas pusilla) differs at the stations according to abiotic conditions. All in all, this study will provide a framework for a better understanding of the interactions between environmental conditions and corresponding pico-phytoplankton communities in arctic pelagic systems.