OBJECTIVE: Citri Reticulatae Pericarpium (Chenpi, CRP) is one of the most used traditional Chinese medicines with great medicinal, dietary and collection values, among which the Citrus reticulata cv. 'Chachi' (Citrus reticulata cv. Chachiensis) from Guangdong Xinhui is the geoherb of CRP. Xinhui CRP in the market was often counterfeited with other varieties or origins, molecular identification method can effectively distinguish different CRP varieties, but it's still a difficult problem to identify the same CRP variety from different origin. It is necessary to discover a new molecular marker to ensure the safe and effective application of Xinhui CRP. METHODS: We selected one of the most studied transcription factor families in Citrus genus, MYB, to design the specific candidate primers on the conserved region. The primers with good band repeatability and high polymorphism were screened for PCR amplification of the test materials, and the genetic similarity coefficient among different families, genera, species, and origins were calculated. The cluster analysis was performed by unweighted pair group method using arithmetic average (UPGMA). RESULTS: A total of ten MYB primers were screened out to identify Xinhui CRP from plants from different family (Panax ginseng and Morus alba), genus (Clausena lansium and Zanthoxylum schinifolium), and species (Citrus reticulata, C. sinensis and C. maxima). Furthermore, two from the ten primers, M1 and M10, were found to distinguish Xinhui CRP from other origins. There were 169, 113, 133 and 134 polymorphic bands in the identification of different families, genera, species, and origins respectively, and the accordingly polymorphism ration were 79.88%, 76.87%, 79.20% and 82.84%. Moreover, M1 was discovered to be the best primer to identify Xinhui CRP from other seven origins, the cluster analysis results based on the genetic similarity coefficients were consistent with the geographical distribution. CONCLUSION This study established a novel molecular identification method according to MYB transcription factor, which can analyze the potential parental relationship of CRP germplasm, as well as identify the quality and origins of Xinhui CPR.