DNA sequences in the chloroplast (trnH-psbA intergenic spacer) and nuclear (ITS) regions were amplified and determined for Huajuhong derived from the peels of the immature fruits of Citrus grandis ‘Tomentosa’ and related medicinal material. These sequences together with the inter-simple sequence repeats (ISSR) markers may be used to differentiate C. grandis ‘Tomentosa’ from other Citrus variants for the prevention of misuse.