The present disclosure provides a molecular marker linked to Fusarium wilt resistance gene in tomato, and a method for obtaining the molecular marker linked to Fusarium wilt resistance gene in tomato. The molecular marker according to the present disclosure has a high specificity, and can be used to identify the resistance to Fusarium oxysporum f. sp. Physiological race 3 quickly and improve the breeding efficiency of the seeds resistant to Fusarium oxysporum f. sp. Physiological race 3. The molecular marker linked to Fusarium wilt resistance gene in tomato according to the present disclosure is prepared simply and has a low production cost. The molecular marker according to the present disclosure can be used to identify the resistance to Fusarium oxysporum f. sp. Physiological race 3, screen the tomato single plant which is resistant to Fusarium oxysporum f. sp. Physiological race 3, and/or determine the purity of hybrid seeds derived from hybridization of the tomato which is resistant to Fusarium oxysporum f. sp. Physiological race 3 and the tomato which is susceptible to Fusarium oxysporum f. sp. Physiological race 3. The molecular marker according to the present disclosure can be also used to prepare a kit, which has the same uses as that of the molecular marker according to the present disclosure.