Curcuma drugs have been used discriminatingly for invigorating blood circulation, promoting  digestion, and as a cholagogic in China.  However, there is confusion about the drug’s botanical origins and clinical uses because of morphological similarity of Curcuma plants and drugs.  Comparative sequencing of  the 18S rRNA gene in nuclear ribosomal DNA (rDNA) and trnK gene in chloroplast DNA (cpDNA) was carried out in order to examine interspecies phylogeny and to identify ultimately Curcuma species.  A total of a hundred of accessions of eighteen species were analyzed.  This resulted in an aligned matrix of 1 810 bp for 18S rDNA and 2 800 bp for trnK.  18S rDNA sequence divergence within the ingroup ranged from 0−0.05%, trnK ranged from 0−0.19%.  One base transversion-substituted site (from cytosine to thymine) was observed from the    upstream of 18S rDNA at nucleotide position 234 in C. kwangsiensis and Japanese population of C. zedoaria which have separated genetic distance to other Curcuma taxa.  Two noncoding regions embedded in trnK intron showed higher variability, including nucleotide substitutions, repeat insertion and deletions.  Based on consensus of relationship, eighteen major lineages within Curcuma are recognized at the species level.  The results suggest that Curcuma is monophyletic with 100% bootstrap support and sister to the genera Hedychium and Zingiber.  The trnK sequences showed considerable variations between Curcuma species and thus were revealed as a  promising candidate for barcoding of Curcuma species, which provide valuable characters for inferring relationship within species but are insufficient to resolve relationships among closely related taxa.