Fruit fly (Diptera: Tephritidae) species are a serious threat for fruit-growers worldwide. The parasitoids (Hymenoptera) are natural enemies of these flies. In this context, the aim of this work was to assess fruit infestation by tephritid flies, both in native and exotic fruit trees, in the Southern region of Rio Grande do Sul (Brazil). Moreover, the incidence of native parasitoids on fly larvae was estimated. Fruits with signals of attack by fruit flies were collected randomly both in the trees and on the ground. From 2013 to 2015, a total of 5729 fruits (194.48 kg) were collected, corresponding to 34 tree species from 16 botanical families. Fruits were taken to the laboratory, individualized, weighted and kept in vermiculite for pupae emergence. Pupae were counted and emerged adults were counted and identified. The association between fruit flies, hosts and parasitoids was determined when only a given species of tephritid emerged. Half of the sampled fruit tree species presented infestation by flies. The main species of tephritid fly was Anastrepha fraterculus. This study showed that natural parasitism rates of fruit flies were low; however, several parasitoid species from the Figitidae and Braconidae families were detected, including Aganaspis pelleranoi, Doryctobracon areolatus, Doryctobracon brasiliensis, Opius bellus, Utetes anastrephae, and Cerchysiella insularis.