Aluminum (Al) toxicity is a major limiting factor for crop growth on acid soils which can be alleviated by Boron (B) supply with unclear mechanism.Precious studies have demonstrated that the root transition zone is most sensitive to Al toxicity, however, it is difficult to distinguish it in the root apex with thicker diameter such as pea (Pisum sativum) than the thinner roots e.g. Arabidopsis thaliana. In this study, we divided root zones taking advantage of the highest conent of pectin in meristem and highest Al sensitivity in root transition zone, localized by brightest immunofluorescence of JIM5 (low-methylesterified pectins) and Morin stain(mobile Al) in root apex of pea (Pisum sativum), respectively. Fluorescent of JIM5 and Morin stain displayed that the brightest fluorescence in the area of 0.5-1.0 mm (meristem) and 1.0-2.5 mm (root transition zone) from the root apex. The zonation of root meristem, transition zone and elongation zone was confirmed by the cell size of the cross-sections of 0.5-1.0, 1.0-2.5, 2.5-5.0 mm root and was consistent with our previous results. Thus root meristem and transition zone are labelled successfully by JIM5 and Morin. The fluorescence intensity increased gradually at different duration of Al exposure (6, 9 and 12 h), which decreased in B-supplied plants. Analysis of Al contents by ICP-AES also showed B-supplied plant had lower total Al content in 1.0-2.5 mm under 12 h of Al treatment. Both the immunofluorescence of JIM5 and the activity of pectin methylesterase enzymes (PME) decreased gradually from the root apex, and the brightest region of JIM5 immunofluorescence and highest activity of PME werelocated in 0.5-1.0 mm (root meristem) under Al exposure which was decreased by B-supply. Therefore, B supply decreases the fluorescence of JIM5 and the activity of PME in meristem and Morin stain in transition zone, and thus alleviates Al toxicity.