Phyllobacterium brassicacearum is a plant growth promoting bacterium (PGPB) that stimulates Brassica napus root morphogenesis in absence of bacterial competition. We evaluated in which extent indigenous bacteria associated with B. napus roots and rhizosphere may interfere with the plant growth promoting ability of P. brassicacearum. Thus, bacteria from B. napus roots and rhizosphere were isolated and co-inoculated with the PGPB at different proportions. The root growth promoting ability of P. brassicacearum was impaired only when it was co-inoculated in low proportion together with the indigenous bacteria. This was not linked to a decrease in its population size on roots. Hence, this study highlights that the efficacy of a PGPB is not primarily dependent on the extent of its root colonization but also depends on its initial size compared to the indigenous bacteria.