In 2022, apple seedlings showed symptoms of damping off with more than 50% disease incidence. The causal organism was isolated from infected seedlings which showed a white-colored mycelium with yellow to pale brown pigmentation on PDA. Additionally, microscopic observation revealed macroconidia and abundant chlamydospores in the pure culture. Based on morphology, sequences of ITS, Tef 1 alpha, and LSU genes the identity of the fungus was confirmed as Fusarium equiseti. Koch's postulates were confirmed by inoculating wheat grains infected with an isolated fungus to healthy apple seedlings. After four weeks of incubation, inoculated seedlings showed damping-off symptoms.To the best of our knowledge, this is the first report of damping-off disease of apple seedlings caused by F. equiseti from India. In-vitro evaluation of eight fungicides and nine botanicals was done against the pathogen through the poison food technique. The result revealed that fungicides Propiconazole at 1 ml L−1, Propiconazole + Difenoconazole at 1 ml L−1, Fluopyram + Tebuconazole at 0.62 ml L−1 and botanicals Curcuma longa at 5–15 % and Allium sativum at 10–15 % exhibited more than 80% inhibition therefore selected for pot studies. In pot studies, drenching of Propiconazole at 1 ml L−1 and Fluopyram + Tebuconazole at 0.62 ml L−1 three times at 15-day intervals yielded 90 % seedling survival followed by Propiconazole + Difenoconazole (83.33 %) and C. longa (5%) crude extract (56.67%). Present findings suggest that drenching of Propiconazole at 1 ml L−1 and Fluopyram + Tebuconazole at 0.62 ml L−1 are effective treatments and recommended to nursery growers for the management of damping-off in apple seedlings.