We studied summer mesozooplankton composition between 2001 and 2009, in the epipelagic zone of the West Spitsbergen Current (WSC) and adjacent areas, which constitute a transition zone between warmer Atlantic and cold Arctic waters. According to hydrography and species composition, this region could be divided into 4 main areas: western and eastern branches of the WSC, the Greenland Sea together with Fram Strait, and the shelf areas of Spitsbergen and the Barents Sea. The most abundant species was Oithona similis and the most important, in terms of biomass, was Calanus finmarchicus; both species were found at all stations. The novel spatial analysis method of principal coordinates of neighbour matrices (PCNM) and the following variation partitioning were applied to disentangle the contributions of environmental variables and spatial differences in explaining mesozooplankton community variation. In spite of the large geographic area covered, environmental factors used in redundancy analysis (RDA) explained 30.6% of zooplankton variability, while the spatial distribution of sampling stations was responsible for 27.2%, and 12.5% was a common share of both predictors, coming from their correlations. We observed a smooth change from dominance of ubiquitous and boreo-Arctic taxa such as O. similis and Triconia sp. in the beginning of the study period towards stronger dominance of boreal taxa such as C. finmarchicus, which was the most abundant species in 2009.