Sequence characterized amplified region (SCAR) markers were developed to selectively detect Korean hwanggi medicine (Radix Astragali) from imported ones from China. The SCAR markers were designed based on the nucleotide sequence of the psbA/trnH intergenic region (cpDNA) and significant bands obtained by inter-simple sequence repeat (ISSR) analysis. The psF/trnH marker was developed was based on the inserted sequence (TAAAA) within all of the Chinese samples (imports and local). Based on UBC 850 primer-amplified specific bands from all Chinese hwanggi medicine, the 15F/15R marker was designed. This primer showed high stability through 6 repeated amplifications, whereas psF/trnH marker showed 50% stability. Therefore, the designed SCAR marker (15F/15R) could be able to identify Korean hwanggi medicine as well as that imported from China.