BACKGROUND: The stink bugs Edessa meditabunda, Piezodorus guildinii, and Diceraeus furcatus (Hemiptera: Pentatomidae) are major pests in the Argentinean core area of soybean production. A detailed molecular genetics comprehension of how these insects perceive odorants and respond to semiochemicals, and how they detoxify chemical pesticides and plant compounds, are essential to improve their management strategies. RESULTS: We first assembled and compared the transcriptomes from E. meditabunda, P. guildinii, and D. furcatus. Regarding sequence similarity, P. guildinii and D. furcatus are closer to each other than E. meditabunda. Then, we characterized the multigene families of odorant binding proteins (OBP) and cytochrome P450 monooxygenases (CYP). A total of 29, 38, and 39 unigenes encoding for OBP were obtained in E. meditabunda, P. guildinii, and D. furcatus, respectively, divided into classical OBPs and plus-C OBPs. A total of 72, 63, and 76 unigenes encoding for CYP were found in E. meditabunda, P. guildinii, and D. furcatus, respectively, which were further classified into 24 families and 47 subfamilies. Finally, we performed RNA interference in vivo by dsRNA injection targeting vATPase A in E. meditabunda, showing a 97% reduction in its expression in comparison to controls, and significant differences in insect survival due to silencing effect. See brief description of the files contents in SuppData.doc CONCLUSION: We reported for the first time the analysis of highly complete E. meditabunda and D. furcatus transcriptomes. We also showed that E. meditabunda is susceptible to RNAi, suggesting that this molecular tool can be exploited in future physiological and functional studies.