The survival and physiological status of a plant-beneficial pseudomonad on the roots of mycorrhizal and non-mycorrhizal pepper were examined. Pepper plants were grown for 20 d in split-root microcosms with one side of the root system mycorrhizal with Glomus deserticola (GD) or Glomus intraradices (GI), while the other side was non-mycorrhizal. Plants with both sides non-mycorrhizal served as controls. The soil was inoculated with a bioluminescence-marked strain, Pseudomonas fluorescens 2–79RL. Due to a ribosomal promoter that has been coupled to a lux gene cassette, P. fluorescens 2–79RL emits light in its exponential growth phase. Previous studies showed that the length of the lag phase of bioluminescence after transfer of soil-cultured cells into rich medium can be used to assess the physiological status of this strain. After 20 d, shoot and root weight of the mycorrhizal plants in comparison with the control plants was decreased by 35% and 45% by GD and GI, respectively, indicating a high carbon cost of the mycorrhizal infection. Mycorrhizal infection was only 6% for GD, whereas it was 40 % for GI. Compared with the non-mycorrhizal plants, GD affected P. fluorescens 2–79RL on the roots only on the side where the fungus was present, but had no effect on the non-mycorrhizal side. On the mycorrhizal side, GD decreased the population density of P. fluorescens 2–79RL by 50 % and its physiological status by one order of magnitude. By contrast, GI decreased both the population density and the physiological status on the mycorrhizal and the non-mycorrhizal side by one order of magnitude. On individual root segments, there was no correlation between the percentage mycorrhizal infection and the population density of P. fluorescens 2–79RL. It is concluded that some mycorrhizal fungi can reduce both the population density and the physiological status of certain bacterial groups in the rhizosphere.