Fusarium wilt disease of watermelon (Citrullus lanatus (Thunb.) Matsum & Nakai), caused by Fusarium oxysporum f. sp. niveum (FON), is one of the limiting factors of worldwide watermelon production. In this study, a Fusarium wilt resistant watermelon JSB, which was derived from a spontaneous mutation of the susceptible Sugar Baby (SB), was used to investigate histopathology. The number and diameter of xylem vessels in the root (10 mm below the shoot base) of resistant JSB plants were significantly higher than those in susceptible SB plants. At 9 days post inoculation (dpi), using the plate assay on Nash-PCNB media, FON could be recovered from 86% of the roots in the symptomless plants of both watermelon lines, and from 55% and 64% of the stem segments (5 mm above the shoot base) in resistant and susceptible plants, respectively. In paraffin and free-hand tissue sections, at 8, 13, and 35 dpi, the xylem of roots and stems close to the soil surface in resistant watermelon JSB plants was also colonised by FON, but to a much lower percentage than the susceptible SB ones. No colonisation below the middle of stems was observed in the resistant JSB plants. The susceptible plants grown in infested soil were all dead by 35 dpi, while the resistant plants remained healthy. These observations suggest that reducing FON colonisation in the vascular systems of the host may contribute to the resistance in JSB. Furthermore, the higher expression of the phenylalanine ammonia lyase (PAL) gene in JSB induced by FON and the effects of PAL inhibitor on the resistance of JSB suggested that PAL is involved in resistance of watermelon to Fusarium wilt pathogen.