We report on the identity of indigenous mycorrhiza forming fungi and rhizosphere/mycorrhizosphere bacterial community carbon source utilization profiles of Scots pine ( Pinus sylvestris L.) seedlings grown in boreal forest humus (O) or illuvial (B) mineral horizon containing microcosm growth systems. Based on rDNA (ITS)-RFLP analyses, a total of 10 fungal RFLP taxa were identified from pre-morphotyped mycorrhizas on 7-month-old seedling roots. Hierarchical cluster analysis, including corresponding RFLPs of known fungal species, confirmed root colonization by eight mycorrhizal species. In the O horizon, roots were colonized by e.g. Suillus bovinus, Suillus variegatus, Cenococcum geophilum, Piloderma croceum, Thelephora terrestris and Russula vinicolor. Mycobiont diversity in the mineral B horizon was lower but included Piceirhiza bicolorata and both Suillus species which produced extensive extramatrical mycelium. In comparison to non-colonized soils, rhizosphere and mycorrhizosphere compartments supported significantly higher numbers of bacteria (mean range 10 8–10 11 cells g −1 fresh weight (fw)). Specific rhizosphere/mycorrhizosphere ‘niche’-linked bacterial communities were detected following multivariate analyses (PCA and CA) of bacterial carbon utilization profiles (Biolog® GN microplate). Distinct preferences for amino and carboxylic acids were identified in mineral B horizon rhizospheres whereas a wider range of carbon sources were utilized in the fungal-dominated mycorrhizospheres irrespective of soil types.