The capacity to bind to biomolecules is considered to be the basis for any physiological role of boron (B). Legume arabinogalactan protein-extensin (AGPE), a major component of the infection thread matrix of legume nodules is a potential B-ligand. Therefore, its role in infection threads development was investigated in Pisum sativum grown under B deficiency. Using the AGPE-specific antibody MAC265, immunochemical analysis revealed that a 175 kDa MAC265 antigen was abundant in +B but much weaker in –B nodule extracts. A B-dependent complex involving AGPE and rhamnogalacturonan II (RGII) could be co-purified using anti-RGII antiserum. Following fractionation of –B nodules, MAC265 antigens were mostly associated with the bacterial pellet. Immunogold staining confirmed that AGPE was closely associated with the surface of rhizobia in the lumen of threads in −B nodules whereas in +B nodules, AGPE was separated from the bacterial surface by a sheath of capsular polysaccharide. Interestingly, colonies of rhizobia grown in free-living culture without B developed low capsule production. Therefore, we propose that B could be important for apical growth of infection threads by strengthening thread wall through a B-dependent AGPE-RGII interaction and by promoting bacterial advance through a B-dependent production of a stable rhizobial capsule that prevents AGPE attachment.