Soils comprise structured biological assemblages and microbial communities must adapt to physical environment and biological constraints. Rhizospheric bacteria called rhizobia interact with roots of legumes to form nodules and perform atmospheric nitrogen fixation. Both plant and bacteria signals contributing to nodule establishment have been shown to play a major role in the specificity of the legume-Rhizobium interaction. The present study aimed to assess if several factors such as cropping systems, N fertilization and application of crop residues affect this specificity. Promiscuous soybean (TGx 1740-2F) was planted in Meru South district (Kenya) every season from March 2007 and three factors were considered: (i) cropping (system monolegume (ML) i.e soybean, association (AS) i.e soybean and maize grown simultaneously or rotation (RO) i.e maize and soybean grown alternately), (ii) Nitrogen fertilization 60 kg.ha-1 (+N or –N) and (iii) maize residues application (+R or –R). Nodulation was assessed and nodules collected during the long rainy season 2008 and the short rainy season 2009. After surface sterilization DNA was extracted and Inter Genic Spacer (IGS) region amplified by Polymerase Chain Reaction (PCR). PCR products were then restricted to obtain Restriction Fragment Length Polymorphism (RFLP) profiles. Results showed that nodulation was not significantly affected by the different factors except N fertilization, regardless the season. Nodule occupancy revealed only 3 main profiles representing 93.6% and 92.5% of all the RFLP profiles obtained from 2008 and 2009 nodules respectively. This suggested a low diversity of native rhizobial strains capable to nodulate the promiscuous variety. The cropping system, N and R application didn't increase the diversity of the rhizobia but results indicated an effect on the distribution of the 3 profiles within the nodules of the plants. Within same treatments, significant differences were found between the two seasons in t