Abstract: In 2023, stem basal rot disease of muskmelon seedlings was found in the muskmelon cultivation base of Qiqihar Agricultural Technology Extension Center. In order to identify the cause of the disease and screen out effective botanical fungicides with high virulence against pathogens, tissue separation method was used to isolate the pathogens from infected stem. Two pathogenic fungi were and purified from diseased seedlings, and were identified as Fusarium oxysporum and Fusarium nirenbergiae by morphological characteristic and ITS-rDNA sequences. Pathogenicity experiments showed that both strains can infect melon seedlings, leading to the occurrence of stem rot disease. Five plant botanical fungicides were accessed the inhibition on the mycelial growth and the toxicity to two fungi. The results showed that all effective concentrations of 20% eugenol, 0.5% matrine and 2.1% carvacrol can inhibit the hyphae growth of two pathogens by more than 30%. The EC₅₀ values of 20% eugenol, 0.5% matrine, 0.5% berberine, 2.1% eugenol, and 80% allicin for F.oxysporum were 9.413, 21.497, 36.670, 48.342 and 48.575 mg·L^-1, respectively. The EC₅₀ values for F.nirenbergiae were 13.768, 14.697, 43.260, 32.475 and 34.158 mg·L^-1, respectively. It indicates that among the five botanical fungicides, 20% eugenol has the strongest virulence against the pathogens of musk melon stem basal rot disease.