Krossfjorden and Kongsfjorden are Arctic fjords on the western side of Spitsbergen. These fjords share a common mouth to the open sea, and both are inXuenced by the input of sediment-rich glacial meltwater leading to decreased surface salinity, increased turbidity and decreased light penetration during summer. Earlier classical taxonomic studies had described the pelagic protistan composition of the Kongsfjorden during summer, revealing the dominance of Xagellates of often unresolved taxonomic origin. Only little information existed on microbial eukaryote composition of the Krossfjorden as well as the bacterial composition of both fjords. The aim of the present study was to analyze and compare surface summertime protistan and bacterial communities in both fjords, using molecular approaches (16S and 18S rRNA DGGE, sequencing). Samples were collected three times a week from the central Kongsfjorden over a 1-month period. Additionally, 10 marine and 2 freshwater sites were sampled within a 1-week period in both Kongsfjorden and Krossfjorden. The central Kongsfjorden revealed a relatively stable protistan community over time with dinoXagellates, chlorophytes and small heterotrophs dominating. In contrast, the bacterial community varied over time and appeared to be correlated with the inXow of glacial meltwater. The Kongsfjorden and Krossfjorden were found to harbor distinctive bacterial and eukaryotic communities. We speculate that diVerences in glacial meltwater composition and fjord bathymetry aVect the surface water properties and therefore the observed spatial variability in the community Wngerprints ; Krossfjorden and Kongsfjorden are Arctic fjords on the western side of Spitsbergen. These fjords share a common mouth to the open sea, and both are inXuenced by the input of sediment-rich glacial meltwater leading to decreased surface salinity, increased turbidity and decreased light penetration during summer. Earlier classical taxonomic studies had described the pelagic protistan composition of the Kongsfjorden during summer, revealing the dominance of Xagellates of often unresolved taxonomic origin. Only little information existed on microbial eukaryote composition of the Krossfjorden as well as the bacterial composition of both fjords. The aim of the present study was to analyze and compare surface summertime protistan and bacterial communities in both fjords, using molecular approaches (16S and 18S rRNA DGGE, sequencing). Samples were collected three times a week from the central Kongsfjorden over a 1-month period. Additionally, 10 marine and 2 freshwater sites were sampled within a 1-week period in both Kongsfjorden and Krossfjorden. The central Kongsfjorden revealed a relatively stable protistan community over time with dinoXagellates, chlorophytes and small heterotrophs dominating. In contrast, the bacterial community varied over time and appeared to be correlated with the inXow of glacial meltwater. The Kongsfjorden and Krossfjorden were found to harbor distinctive bacterial and eukaryotic communities. We speculate that diVerences in glacial meltwater composition and fjord bathymetry aVect the surface water properties and therefore the observed spatial variability in the community Wngerprints