Boron (B) is an essential micronutrient for vascular plants. The function of B has been demonstrated to cross-link monomeric rhamnogalacturonan II (mRG-II) to form dimeric RG-II-borate (dRG-II-B), and thus to stabilize plant cell walls. The dRG-II-B to total RG-II ratio in the cell walls of pumpkin hydroponically grown under various low-B conditions was analyzed to evaluate its applicability to the diagnosis of plant B deficiency. The dRG-II-B ratio in cell walls ranged between approximately 0.9 in B-sufficient tissues and approximately 0.15 in severe B-deficient tissues, reflecting the B nutritional status of tissues. This result indicates that the degree of B shortage in plant tissues is very likely to be diagnosed by the dRG-II-B ratio in cell walls.