Phaseolus vulgaris L. (Leguminosae) forms symbioses with arbuscular mycorrhizal fungi (AMF) and nitrogen-fixing rhizobia (NFB). The tripartite relationship uses molecular singals to establish intracellular symbioses in roots. The goal of this study was to determine if Rhizobium tropici CIAT 899 and exogenous riboflavin (vitamin B2) have an effect on AMF species selection and root colonization of P. vulgaris. Using SSU rRNA fragment amplification of DNA extracted from P. vulgaris roots, we found that the presence of R. tropici altered the relative distribution of AMF species. Dominikia bernensis (Ohel) was the most abundant AMF species in P. vulgaris roots but when R. tropici was co-inoculated, Glomus species dominated. Rhizobacteria such as R. tropici, secrete riboflavin and could affect AMF symbiosis. Addition of 50 μM riboflavin to P. vulgaris, increased plant growth (28%), dry nodule weight (18%), AMF colonization (248%) and mycorrhizal vesicle frequency (56%) in bean roots. 3.12 and 12.5 µM riboflavin favored the presence of Glomus macrocarpum in P. vulgaris roots. This work provides de basis for further investigation of rhizobial and mycorrhizal co-inoculation of Phaseolus vulgaris bean.