Citrus trees are often exposed to severe infectious diseases. Mal seeco caused by Phoma tracheiphila (Petri) Kantschaveli and Gikashvili is one of the most destructive fungal diseases of lemons (Citrus limon Burm. F.). In the present study antioxidant enzyme activity in different mal secco-resistant and susceptible citrus rootstocks including Cleopatra mandarin (C. reshni Tan.), sour orange (C. aurantium L.), rough lemon (C. jambhiri Lush.), Volkameriana (C. volkameriana Tan. and Pasq.), Carrizo citrauge (Poncirus trifoliata L. Raf. X C. sinensis L. Osbeck) and trifoliate orange (P. trifoliata) was investigated. Possible differences in constitutive levels of these antioxidant enzymes and correlations between enzyme levels and mal secco caused by P. tracheiphila were examined. Among the rootstocks, Cleopatra mandarin was found to be resistant to mid secco, whereas rough lemon, sour orange and trifoliate orange were highly susceptible. Total peroxidase (TPX; EC: 220.127.116.11) activity increased in all infected rootstocks. Ascorbate peroxidase (APX; EC: 18.104.22.168) activity increased in most of the rootstocks and no correlation was found between catalase (CAT; EC: 22.214.171.124) activity and mal secco resistance. This study indicates that overall TPX activity is upregulated and APX activity is up- and down-regulated depending on the type of rootstock in response to P. tracheiphila infection.