Wilt disease caused by Fusarium oxysporum f. sp. capsici is a major problem of chilli pepper production worldwide that calls for a better understanding of defensive mechanisms in the chilli plant. We used a proteomic technique to investigate protein responses of chilli pepper to F. oxysporum f. sp. capsici. Two cultivars of resistant (Mae Ping 80) and susceptible (Long Chilli 455) plants were cultured in vitro. Chilli plants at 6-week growth were then infected with a suspension of F. oxysporum f. sp. capsici or distilled water used as a control. After 48 h of infection, proteins were extracted and analysed using 2DE to identify the responsive proteins. At least 9 spots were differentially expressed in the resistant cultivar (5 increasing, 4 decreasing) and 1 supplementary; while 15 increasing, 11 decreasing, and 11 supplementary protein spots were found in the susceptible cultivar. These proteins were then identified by MALDI-TOF MS combined with bioinformatics methods. Some of the induced proteins e.g., NADPH HC toxin reductase, serine/threonine protein kinase, and 1-aminocyclopropane-1-carboxylate synthase 3 are involved in plant defence mechanism. In order to determine the Fusarium wilt protective proteins in chilli plant, the protein patterns of healthy resistance were compared with those of susceptible cultivars. Interestingly, resistance showed higher expression of proteins related to ROS detoxification. Moreover, the ability of chilli plant to resist Fusarium wilt disease was related to the expression of non-inducible immunity 1 protein.