Abstract:[Background] Soil microorganism is an important component of soil organisms and participates in key biochemical cycles in soil ecosystem. However, we still poorly understand on soil microorganisms in permafrost soils in cold temperate regions. [Objective] To study the microbial diversity and community structure of the permafrost in the Greater Khingan Mountains. [Methods] high-throughput sequencing technology was employed to analyze the soil bacterial diversity and community structure which were taken from Huzhong National Nature Reserve in the Greater Khingan Mountains of northern Heilongjiang. [Results] The composition of the soil bacterial dominant phyla were basically the same in the Larix gmelinii and Pinus sylvestris forest. At the level of the phylum, the dominant phyla were Verrucomicrobia, Proteobacteria, Acidobacteria, Planctomycetes, Chlorobi, Parcubacteria, Actinobacteria, Bacteroidetes, Firmicutes, Gemmatimonadetes, of which Verrucomicrobia in Pinus sylvestris forest permafrost has relatively high abundance compared with Larix gmelinii forest permafrost. Alpha diversity analysis revealed that the species diversity of the Larix gmelinii permafrost in the frozen soil is higher than that in the Pinus sylvestris permafrost. Moreover, the compositions and structures of soil microorganisms of the two forest types were quite different. [Conclusion] These findings are intended to provide data support for an in-depth understanding of the soil microbial community structure and influencing factors in the permafrost area of the Greater Khingan Mountains.