Wampee [Clausena lansium (Lour.) Skeels] was originally native to the southern part of China, and had a long history of cultivation. Wampee has been an important species in the development of the fruit breeding program in the genus Clausena, family Rutaceae. In addition to fruit characteristics and bark color, it is difficult to distinguish different varieties of wampee, more difficult of identification of seedling stage. In this study, we determined and analyzed the complete chloroplast genome of Jixin, seedless, and sweet wampee varieties. By comparison, it was found that the sweet wampee is 150 bp less than the other two varieties. We designed a pair of specific primers to distinguish between sweet wampee and other varieties, and it also has better discriminating ability through the analysis of seedlings. The complete chloroplast genome will provide valuable information for the development of highly variable DNA markers for future variety identification and population analysis studies of wampee.