Alternaria sp. is one of the most important pathogens on Citrus that cause brown spot on tangerines, leaf spot on rough lemon and black rot on harvested fruits. This pathogen causes leaves drop in susceptible varieties and is considered as a limiting factor for production in humid areas. On the one hand, due to high damage of the disease (because of leaves fall and also the decrease of quality and quantity of product) and on the other hand, due to the ineffectiveness of chemical and cultural control methods against this disease, identifying clones and varieties resistant to the disease is very important. Therefore, the purpose of present research is the study of the reaction of different Citrus varieties against Alternaria sp. in order to identify better and more tolerant commercial varieties against this fungus. To fulfil this research, 24 cultivars and species of Citrus were selected. Brown spot and black rot causal agents from Citrus leaves and fruits were isolated and after doing pathogenicity test, in vivo (seedlings in the greenhouse) and in vitro (separate leaves in the laboratory) tests were used to study the reaction of the varieties. Results showed that the most Alternaria sp. isolates from Citrus leaves and fruits have a high pathogenicity on Page cultivar. Statistical analysis of the sensitivity level of the cultivars to the fungus in in vivo test showed that there is a statistically significant difference between the cultivars (P<0.01), and in the meanwhile, Limequat and Owari Satsuma and Iwasaki mandarin cultivars had the highest resistance rate to the disease. Hernandina, Oronules, Clemen-Ruby, Marisol and Ortaique-Tangor mandarins and Moro blood orange were also recorded with relatively low leaf infections as semi-resistant or tolerant cultivars. Star ruby, Minneola, Orlando, Page, Washington navel, Valencia, Tarako and Miyagawa were highly infected and categorized as sensitive cultivars. In in vitro test, cultivars were divided into six distinct groups which validated the in vivo test results with a few changes. So, some of the genotypes of the mandarin group (Owari Satsuma, Iwasaki and Clementines) and Limequat hybrid which had high resistance to Alternaria brown spot may be new options for planting in the future.