To understand the relationships between understory bamboos and soil properties in a Betula ermanii boreal forest, we investigated microbial community structures with Sasa kurilensis present and removed by using Next-generation sequencing. The presence of understory S. kurilensis strongly affected soil properties, such as total carbon, total nitrogen, nitrate and C:N ratio as well as the relative soil moisture. There were also notable differences in the fungal and bacterial communities between the plots. Among fungal communities, the relative abundance of phylum Ascomycota in libraries was 13.9% in the Sasa-intact plot, while it was only 0.54% in the Sasa-removed plot. Most abundance value of phylum Ascomycota was attributed to family Pezizaceae. We found that the Pezizaceae, known as mycorrhizal fungi, was related to the amount of total carbon in the Sasa-intact plot. As for bacterial communities, there were significant differences in the abundance of phyla Actinobacteria, Proteobacteria and Planctomycetes between the Sasa-intact and Sasa-removed plots. Furthermore, the results suggested that some species of the phylum Planctomycetes tended to occur in the presence of S. kurilensis. Taken together, these results suggest that the presence of S. kurilensis affected the microbial communities and soil properties in a B. ermanii boreal forest.