Virus-bacterium interactions were investigated in the pelagic and benthic habitats in a set of lakes along an altitudinal gradient in the subarctic northern Sweden. Viral and bacterial abundances showed a significant variation between the lakes, with the highest benthic microbial abundances recorded in a high-altitude lake [993m above sea level (a.s.l.)], whereas the highest pelagic microbial abundances were found in a low-altitude lake (270ma.s.l.). In the pelagic habitat, there was also a distinct difference in microbial abundances between the summer-autumn and the winter sampling occasion. A positive relationship was noted between viruses and bacteria in both the pelagic and the benthic habitats. Visibly virusinfected bacterial cells were uncommon in the pelagic habitat and undetectable in the benthos. Both lytic and lysogenic pelagic viral production rates were undetectable or low; thus, a possible explanation for the relative high viral abundances found in the water column could be an allochthonous input of viruses or release of sediment-derived viruses. Overall, our results provide novel information about the relevance of viruses in the subarctic region and indicate that viruses play only a minor role in the nutrient and carbon cycling in the microbial communities of subarctic lakes.