Aims and Background It has been shown that rhizodeposition of organic compounds shapes rhizosphere microbial communities, and that soil pH regulates spatial distribution of bacteria at field to continental scales. Even though rhizospheric pH displays high variability, possible links between pH and bacterial biogeography at the rhizosphere scale remain largely unknown. The aim of this study was to document the spatial distribution of bacterial communities in relation to soil pH around roots. Methods Pinus pinaster seedlings were cultivated in thin mini-rhizoboxes with and without ectomycorrhizal inoculation (Rhizopogon roseolus). After two months, millimetre-scale mapping of the following parameters were performed on 18 cm2 zones: presence of roots and mycorrhizae; soil pH, using non-invasive planar optodes; and seven taxonomic groups of bacteria, using Q-PCR. Results Soil pH varied considerably, from 4.0 to 7.3, as did bacterial phyla (variation coefficient up to 112%) in the mapped zones. The variability was systematically higher in soil exposed to mycorrhizal roots, and the spatial patterns of bacterial phyla were apparently related to soil pH, root and mycorrhizal distribution. Conclusion Our study is the first to document bacterial biogeography at the root system scale and suggests a key role of rhizosphere pH in structuring bacterial communities as related to either roots or ectomycorrhizae.