Leaf spot disease of rough lemon and brown spot disease of tangerines caused by distinct pathotypes of Alternaria alternata, are the major fungal diseases of citrus. The pathogenicity and specificity for the pathogens of Alternaria leaf spot and brown spot diseases are associated with the production of different host-specific toxins designated as ACR- and ACT-toxins. This review summarizes the recent progress on elucidation of role of host-selective toxins in the pathogenicity of these citrus diseases.