In the south of Bahia state, a large part of the native Atlantic Forest areas has been modified for the cultivation of cocoa (Theobroma cacao). These crops are cultivated under the shade of the canopy of native trees, a system locally known as the “cabruca” agroforestry system. This study aimed to evaluate the relationship of Odonata assemblages (adults and larvae) in cocoa farming areas and to identify the relationships of these species with local and spatial environmental variables of the monitored sites. Altogether, adult and larvae were sampled at 22 sites. Physical and physicochemical water variables were recorded for each site. A total of 1336 dragonflies were collected, of which 20 were Zygoptera species and 30 were adult Anisoptera representatives. The different life stages were related to environmental variables such as conductivity, watercourse channel width, and dissolved oxygen. The space predictors were also associated with the assemblages, mainly for adults. The present study identified that cabruca areas maintain a great diversity of dragonflies, including species that are considered to be forest specialists and more sensitive to landscape changes. The characteristics of this cropping system are considered to be favorable for the conservation of the biodiversity of the Atlantic Forest.