Four members of Fusarium solani species complex (FSSC), F. cucurbiticola, F. petroliphilum, F. falciforme and F. keratoplasticum, cause foot, crown, stem and fruit rot in cucurbits. Although previous studies revealed that F. cucurbiticola was the pathogen causing crown and fruit rot in Taiwan melons, these are unreliable in assessing FSSC infection in cucurbits in Taiwan. We collected 47 FSSC isolates from the stem or fruit rot of bitter gourd, cucumber, luffa, melon and pumpkin, and three FSSC isolates from pumpkin seeds. Eleven pumpkin fruit rot isolates and two pumpkin seed isolates could not infect cucurbit seedlings. Luffa seedlings were tolerant to most FSSC isolates. None of the FSSC isolates could infect cucumber fruits and showed variable virulence in different cucurbit fruits. In addition, only certain FSSC isolates could be amplified by specific primers for F. cucurbiticola and F. petroliphilum. Multilocus sequence typing analyses separated FSSC isolates from the stem or fruit rot or seeds into three molecular groups with high bootstrap values: Group I isolates were F. petroliphilum (FSSC1), Group II isolates were F. solani‐melongenae (FSSC 21) and Group III isolates were F. falciforme (FSSC 3+4). The FSSC isolates amplified by specific primers for race 2 belonged to F. petroliphilum; however, the FSSC isolates amplified by specific primers for race 1 were not F. cucurbiticola. To our knowledge, the three species of the FSSC are novel causative agents in Taiwan.