Plant genotypes differ in their capacity to grow in soils with low manganese (Mn) availability. The physiological mechanisms underlying differential tolerance to Mn deficiency are poorly understood. To study the relationship between Mn content in soil, plant genotypes, and rhizosphere microorganisms in differential Mn efficiency, two wheat (Triticum aestivum L.) cultivars, RAC891 (tolerant to Mn deficiency) and Yanac (sensitive), were grown in a Mn-deficient soil to which 5, 10, 20 or 40 mg Mn kg–1 were added. The shoot dry matter of both cultivars increased with increasing Mn addition to the soil. At all soil Mn fertilizer levels, the tolerant RAC891 had a greater shoot dry matter and a higher total shoot Mn uptake than the sensitive Yanac. The concentration of DTPA-extractable Mn in the rhizosphere soil of RAC891 at Mn20 and Mn40 was slightly lower than in the rhizosphere of Yanac. The population density of culturable microorganisms in the rhizosphere soil was low (log 6.8–6.9 cfu (g soil)–1) in both cultivars and neither Mn oxidation nor reduction were observed in vitro. To assess the non-culturable fraction of the soil microbial community, the ribosomal intergenetic spacer region of the bacterial DNA in the rhizosphere soil was amplified (RISA) and separated in agarose gels. The RISA banding patterns of the bacterial rhizosphere communities changed markedly with increasing soil Mn level, but there were no differences between the wheat cultivars. The bacterial community structure in the rhizosphere was significantly correlated with the concentration of DPTA-extractable Mn in the rhizosphere, fertilizer Mn level, shoot dry matter, and total shoot Mn uptake. The results obtained by RISA indicate that differential tolerance to Mn deficiency in wheat may not be related to changes in the composition of the bacterial community in the rhizosphere.