Fludioxonil is widely used as a fungicide in agriculture to protect crops from fungal diseases. It is applied to seeds, soil, and foliage to control pathogens such as Fusarium, Rhizoctonia, and Botrytis, which can severely impact crop yield and quality. Its mode of action involves disrupting fungal cell membrane integrity, making it effective even at low concentrations.

In post-harvest applications, fludioxonil is used to prevent spoilage and extend the shelf life of fruits and vegetables by inhibiting fungal growth during storage and transportation. It is particularly effective on grapes, cherries, and citrus fruits.

Additionally, fludioxonil is utilized in non-agricultural settings, such as in wood preservation and as a protective treatment for textiles, to prevent mold and mildew formation. Its stability and low toxicity to non-target organisms make it a preferred choice in integrated pest management programs.