Bacteria are one of major components of the marine food web and play an important role in marine ecosystems. High abundance of bacteria has been reported in Kongsfjorden, a typical Arctic fjord on the northwestern coast of Svalbard.Freshwater input from glaciers inevitably affects the bacterial communities in Kongsfjorden during the summer season.Community fingerprint analysis of surface water and sediment samples collected in the summer of 2011 was performed using a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach. Sediment bacterial communities showed a higher diversity index than communities in surface seawater.Because of the influence of terrestrial freshwater input, communities in sediments from stations deeper than 200 m differed from communities in surface seawaters and communities in sediments from stations shallower than 40 m. Differences in planktonic bacterial community compositions were also observed between the inner and outer part of the fjord.Sequences of DGGE bands fell into six major lineages of the domain Bacteria, including alpha, gamma, and delta Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes.In contrast to a similar abundance of planktonic bacteria between the outer and inner part of Kongsfjorden on quantitative PCR (QPCR) assay, there was a higher abundance of the Roseobacter clade in the outer part compared with the inner part of the fjord.Results suggest that compared with the outer part, the inner part of Kongsfjorden is more affected by terrestrial freshwater input, resulting in differences in bacterial community composition as well as in abundance of specific bacterial species.In addition, comparison with a similar investigation in the summer of 2007 showed lower diversity of planktonic bacteria in 2011.Whether this finding reflects the response of bacterial communities in Kongsfjorden to global climate change remains uncertain.