The Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae), is considered one of the most economically damaging pests of citrus orchards in Spain. Insecticide treatments for the control of this pest are mainly based on aerial and ground treatments with malathion bait sprays. However, the frequency of insecticide treatments has been increased in some areas of the Comunidad Valenciana in the last years, because of problems with the control of C. capitata. We have found that field populations from citrus and other fruit crops from different geographical areas in Spain showed lower susceptibility to malathion (6- to 201-fold) compared with laboratory populations. More importantly, differences in susceptibility could be related to the frequency of the field treatments. A resistant strain (W), derived from a field population, and a susceptible laboratory strain (C) were maintained in the laboratory. The W strain showed cross-resistance to the organophosphate fenthion (10-fold) but not to spinosad. Enzymatic assays showed that acethylcholinesterase activity was less inhibited in vivo by malathion and in vitro by malaoxon (active form of malathion) in adult flies from the W-resistant strain. Experiments to evaluate the effects of synergists revealed that the esterase inhibitor S,S,S-tributyl phosphorotrithioate (DEF) partially suppressed malathion resistance. Thus, target site insensitivity and metabolic resistance mediated by esterases might be involved in the loss of susceptibility to malathion in C. capitata. Nonetheless, additional biochemical and molecular studies will be required to confirm this hypothesis.