The establishment of safe and effective methods for controlling fungal diseases is an urgent issue in agriculture and forestry. Fungicide research has provided a wide range of products with new modes of action. Extensive use of these compounds in agriculture enhances public anxiety due to the harmful potential for the environment and human health. Moreover, the phytotoxic effects of some fungicides are already recognized but still little is known about their influence on the photosynthetic apparatus and plant physiology. This review provides an understanding of the mechanisms of action of fungicides, mechanisms of fungicide resistance development, and the phenomenon of phytotoxicity.