Plant growth‐promoting bacteria (PGPB) have been reported to stimulate root morphogenesis. To improve our knowledge of the PGPB effect, the early modifications of Brassica napus root system architecture induced by the PGPB Phyllobacterium sp. (29‐15) were analysed. Plants were grown in Petri dishes on a vertical medium supplemented with variable doses of Phyllobacterium sp. in gnotobiotic conditions. Root system elementary variables were measured in a nondestructive manner and the distribution of the bacteria throughout the primary root was quantified. Phyllobacterium sp. in doses from 3 × 107 to 3 × 108 colony‐forming units ml−1 significantly promoted B. napus total root length up to 50% by increasing both lateral root density throughout the primary root and growth rate of mature lateral roots. The primary root was progressively colonized by the bacteria from the tip to the base and the number of colonizing cells was positively correlated with the inoculum density. • Relationships between inoculum density, root colonization and root system architecture emphasized the relevance of this approach to specify PGPB effects on plants.