The landscape at Samoylov Island is characterized by permafrost and permafrost related processes that create the typical polygonal micro structures of wet tundra landscapes. These micro-morphologic structures strongly affect surface characteristics such as moisture content and vegetation cover. The polygonal structures usually consist of wet centers surrounded by elevated dry rims that vary in size and moisture content. Some structures show well developed rims and small centers, while others are dominated by wet areas. Several polygon centers consist of peat while other form small ponds. A few structures are affected by thermokarst erosion and form complex lake structures. These microscale landscape variations affect the ratio of dry and wet areas on a larger scale. This ratio is critical to sensible and latent heat exchange processes between soil surface and atmosphere. Thus, small scale variations of polygonal landscape features affect larger scale energy balance processes. This work concerns simultaneous eddy-covariance measurements of sensible and latent heat fluxes and their variations due to small scale differences in surface morphology on Samoylov Island. The first eddy-covariance station was erected in spring 2007 on the west side of the island. In summer 2008, a second, mobile eddy-covariance system was constructed to gather parallel flux measurements across the island. The first eddy-system served as the reference station. Three different measurement locations along a west-east transect across the island were established for the mobile system. The first measurement location is dominated by wet polygonal structures, while the second is characterized by dry, well-developed polygon rims. The third location is situated within an area of free water bodies such as small ponds and thermokarst lakes. The measurement period covers six weeks while the interval of data collection at each location was seven days. Hence every measurement location was measured twice by the mobile station. Both eddy-covariance systems were calibrated against each other while measurements occurred at the same location. Differences in sensible and latent heat fluxes were observed within the wet polygonal tundra site, although landscape variations are very small. In particular, these differences were observed during clear sky conditions, when the difference in the energy flux partitioning is at a maximum between dry and wet surfaces. The most evident differences in sensible heat fluxes were measured at location two, where dry surface conditions are dominant. At this location, the sensible heat flux is up to 20% higher than at the reference station. Differences in latent heat fluxes could be observed at the third measurement location, where free water bodies characterize the surrounding area. At this location, the latent heat flux is up to 30% lower compared to the reference station. The first results indicate that microscale surface variations of the polygonal tundra affect larger scale heat flux processes.