Organic farmers have the opportunity to use pesticides and fungicides on their crops, just like conventional farmers. Organic farmers choose from organic certified pesticides and fungicides, which are outlined by the USDA Certified Organic program. According to Scientific American, there are more than 20 options that qualify for U.S. Organic Standards. Some of these options include copper and sulfur anti-fumigants and the naturally occurring Bt toxin. Even in the case of organic and natural pesticides, you should always be safe, take the proper precautions and follow application directions before use.
Farmers use various pesticides in agriculture, see list of definitions.