Watermelons are grafted to prevent soil-borne diseases such as Fusarium wilt (FW) and increase their resistance to abiotic stress. Root-knot nematodes (RKN) are a contributing factor to economic loss in several cucurbits, including watermelon. Growing resistance varieties is an effective way to reduce the damage caused by soil-borne diseases. Resistance evaluation was performed on 50 watermelon lines to select rootstocks resistant to FW and RKN. Fusarium oxysporum f. sp. niveum race 2 was inoculated into 10-day-old seedlings using a root dipping method, and resistance was evaluated for four weeks. The 37-day-old watermelon seedlings were inoculated with Meloidogyne incognita and evaluated 60 days later. Three lines (IT199860, PI296341-6, and PI532811) were resistant to FW race 2, while one line (PI494527) was moderately resistant. Three lines (PI296341-5, PI457916-2, and PI457916-5) were RKN resistant. The PI296341-6 line was selected for its resistance to FW and moderate resistance to RKN. These findings imply that the identified resistant lines can be used in rootstock breeding programs against FW and/or RKN.