Nitrogen nutrition often remains a factor limiting yield and seed protein content of pea crop. As a legume, pea acquires N from two different pathways, symbiotic N2 fixation and soil mineral N absorption by roots. Our main aim was to assess if the bacterial partner, Rhizobium leguminosarum biovar viciae (Rlv), may be a limiting factor of pea N nutrition and seed yield. We show that Rlv populations are genetically polymorphic and that their genetic structure varies among soils. Crop management, such as long-term maize monoculturing, has an impact on the diversity of soil Rlv populations. Moreover, the structure of symbiotic populations varies according to pea genotype and over the growth plant cycle. The plant seems to carry out differential regulation of nodule number according to bacterial genotype. Correlation between functional and genetic variability of Rlv was found. The Rlv genotype influences nodule morphogenesis and biomass partitioning between the different plant compartments. Two contrasted symbiotic phenotypes were pointed out: the BNO (“Big NOdule”) phenotype characterized by reduced number of very large nodules, high nodule biomass and reduced root and shoot biomass as compared with the SNO (“Small NOdule”) phenotype characterized by higher number of small nodules, lower nodule biomass and generally more developed roots and shoots. Field studies showed that a high frequency of BNOs may reduce yield and seed protein content of the crop. Thus, the genetic variability of nodule populations may contribute to variability of nitrogen nutrition and pea growth, with an impact on yield.