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Boreal forest encompasses approximately 30% of the terrestrial carbon (C) storage, representing an important hotspot of C transformations mediated by soil microbial communities in the changing environment. However, our understanding of the microbial community characteristics and the core components of soil microbiome in different succession scenarios of boreal forest is still limited. Here, we compared the diversity, activities and community composition of both bacteria and fungi between upland and swamp boreal forest soils. The microbial diversity and activity were remarkably lower in swamp than upland soils. The bacterial and fungal community compositions were significantly different between the swamp and upland soils. Linear Discriminant Analysis Effect Size analysis identified Firmicutes and Ascomycota as molecular markers for the swamp while Actinobacteria and Mucoromycotina for the upland. Molecular ecological networks revealed significantly less modules and putative keystone species of bacteria and fungi in swamp than in upland soils. The differences in soil microbiome profiles between the swamp and upland sites of boreal forest were attributed to soil moisture content, soil pH and nutrients. Our results suggested that the soil microbial community composition and structure significantly changed across the different succession stages of the boreal forest biome.