Remove infected foliage and flowers as soon as possible. Cut affected foliage from the plant with sharpened and sterilized pruning shears. Destroying the removed plant matter prevents the Botrytis fungal spores from spreading to other plants. After pruning the diseased foliage, wash the pruning shears in a solution of warm, soapy water and dry them with a soft cloth. Moisten a second cloth with rubbing alcohol and rub the blades to kill any lingering Botrytis spores.
Infected moth orchids may spread Botrytis spores to surrounding surfaces. Disinfecting these surfaces prevents nearby plants from infection. The Saint Augustine Orchid Society recommends wiping down any hard surfaces around infected orchids with a broad-range disinfectant, fungicide, viricide and algaecide. Create a homemade disinfectant solution by mixing 1/4 cup household bleach with 2-1/4 cups water. Discard any unused bleach solution.
Botrytis spores linger on the moth orchid even after removal of the infected foliage and flowers. Wipe down the orchid's stems and foliage with a copper-based fungicide and bactericide. Always use fungicide products according to package instructions to avoid injury to yourself or your Phalaenopsis orchid. Copper-based fungicide products are not suitable for use on all parts of the moth orchid. Never apply fungicide to an orchid's flowers unless the product instructions explicitly direct.
Once the Botrytis is controlled, prevent future infections. Move the moth orchid to a spot offering better air circulation. Use a fan if necessary. Water moth orchids in the early morning and avoid wetting their foliage. Leaving an orchid's foliage wet overnight invites fungal disease. Provide daytime temperatures between 70 and 82 degrees and nighttime temperatures above 60 degrees. If the black spots reappear, swab the affected blossoms with a cotton ball dampened with hydrogen peroxide.