Planktonic bacteria play key role in biogeochemical cycles and energy flow in marine ecosystems. However, our knowledge of the extent and character of bacterial diversity in polar marine environments is still limited. Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess the diversity of planktonic bacteria in the arctic Canada Basin, and Kongsfjorden in Spitsbergen. The V3 region of the 16S rRNA gene was amplified from seawater samples collected from the upper water column. The number of bacterial 16S rRNA sequences obtained from each sites varied from 7433 to 9218. In the Canada Basin, the most abundant bacterial groups in two sites of water at 10m depth were the Proteobacteria (mainly Alphaproteobacteria), Actinobacteria, Bacteroidetes and Cyanobacteria. Different bacterial communities were observed in the deeper water (80 or 100m depth) at the two sites. The Proteobacteria and Bacteroidetes also formed the dominant bacterial groups in surface water of Kongsfjorden. However, Gammaproteobacteria accounted for more than 90% of the Proteobacteria.