We determined the actual (no tryptophan, Trp, addition) and potential (Trp 0.1 g l⁻¹ added) production of indolic and phenolic compounds produced in different culture media by Paenibacillus polymyxa strains which had been isolated from different proximity to wheat roots. The production of indole-3-acetic acid (IAA) and related indolic metabolites by all strains tested was greatly enhanced upon Trp addition, suggesting that Trp is important as IAA precursor. A gradual decrease in potential IAA and an increase in potential indole-3-ethanol and indole-3-lactic acid production by strains isolated from nonrhizosphere soil (NRS) over rhizosphere soil (RS) to the rhizoplane (RP) were obtained. The NRS strain showed also a higher (potential) production of oxidized compounds such as indole-3-carboxylic and benzoic acid besides IAA. The determined metabolic differences indicate together with previous results on genetic and physiological parameters of P. polymyxa populations that plant roots select different P. polymyxa subpopulations. Our results suggest that the selected genotypes are differentially adapted to the decreasing oxygen pressure from NRS to RP. Possible effects of the probably microhabitat-specific metabolic profiles of the P. polymyxa isolates for plant growth are discussed.