Plant cell walls, which are mainly composed of pectin, play important roles in plant defence responses to pathogens. Pectin is synthesised in a highly esterified form and then de-esterified by pectin methylesterases (PMEs). Because of this, PMEs are directly involved in plant defence. However, the molecular mechanisms of their interactions with pectins remain unclear. In this study, we compared the expression level and enzyme activities of PMEs in a banana Cavendish cultivar (Musa AAA 'Brazilian') inoculated with Fusarium oxysporum f. sp. cubense pathogenic races 1 (Foc1) and 4 (Foc4). We further examined the spatial distribution of PMEs and five individual homogalacturonans (HGs) with different degree of pectin methylesterification (DM). Results suggested that the banana roots infected with Foc1 showed lower PME activity than those infected with Foc4, which was consisted with observed higher level of pectin DM. The level of HGs crosslinked with Ca2+ was significantly higher in roots infected with Foc1 compared with those infected with Foc4. Therefore, banana exhibited significantly different responses to Foc1 and Foc4 infection, and these results suggest differences in PME activities, DM of pectin and Ca2+-bridged HG production. These differences could have resulted in observed differences in virulence between Foc1 and Foc4.