In this study, we investigated prokaryotic communities along small-scale vegetation gradients in a dry arctic tundra in Northern Sweden. The abundance and coarse-scale phylogenetic composition of the prokaryotic communities were analyzed using fluorescent in situ hybridization coupled with catalyzed reporter deposition, and the detailed community composition was analyzed using the high-throughput sequencing. The number of prokaryotic cells increased with increasing vegetation cover, mainly as a function of increased amounts of soil carbon and moisture. Based on the microscopic analysis, Archaea, Acidobacteria and α-Proteobacteria constituted ca. 33 %, 14 %, and 11 % of prokaryotic cells, respectively. The high-throughput sequencing showed that the prokaryotic community composition significantly changed along the vegetation gradients, and that soil pH was a good predictor of the composition. Our study showed that the aboveground vegetation significantly influenced the soil prokaryotic community, which in turn could have influences on subsequent soil decomposition processes in the dry arctic tundra ecosystems.