BACKGROUND The litchi fruit borer, Conopomorpha sinensis Bradley, is one of the most destructive pests of litchi and longan fruits in south-east Asia and southern China, yet the molecular biology and physiology of this pest remain poorly understood. Control of this insect pest may be achieved by interfering with its recognition of host plants. RESULTS In this study, two cDNAs encoding CsGOBP1 and CsGOBP2 were identified from the antennae of C. sinensis, and a comparative study on these two C. sinensis GOBPs (CsGOBPs) was conducted. The secondary structure of these two CsGOBPs mainly consists of six α-helices, but three-dimensional structural predictions of CsGOBP1 and CsGOBP2 indicated significant difference in the final 3D models. Results in real-time PCR assays indicated that the two CsGOBPs had different tissue- and sex-dependent expression patterns. A competitive binding assay revealed that CsGOBP1 considerably prefer the component exhibited in Guiwei or Feizixiao litchi cultivar, while CsGOBP2 bind to general volatile components from nine litchi cultivars. Additionally, ethyl acetate has higher binding affinities to CsGOBP2 protein than to CsGOBP1, and has remarkable attraction to female C. sinensis moths in Y-tube olfactometer assays. CONCLUSION These results strongly suggest functional difference between these two CsGOBPs in perception of host plant odourants.