Abstract: The classification of Citrus is still a scientific problem unresolved because of apomixes，asexual variation，and interspecific hybridization in the genus Citrus. To use matK，rbcL，and them together to identify Citrus and its closely related genera，the chloroplast matK and rbcL sequences of 59 accessions were analyzed，the inter- and intraspecific genetic distances were calculated，and the phylogenetic trees of all the accessions tested were constructed based on the obtained distance data. The results indicated that matK and matK + rbcL could be successfully used to identify Citrus and its related genera. However，at the species level，matK，rbcL and their combination（matK + rbcL）only have correct identification frequency of 55.9%，37.3%，83.0% respectively. Compared with the single fragment，matK + rbcL was shown to be more powerful，implying that it can be used to identify the species of Citrus and its related genera.

Key words: Citrus, related genera, matK, rbcL, DNA barcode