This study was undertaken to develop a technique of discrimination using SSR makers in boxthorn cultivars.Forty one boxthorn cultivars, which were collected from Korea and China, were evaluated by 10 SSR markers. Total of 61alleles were detected, ranging from 3 to 13 with an average of 6.1 alleles per locus. The averages of gene diversity and PICvalues were 0.482 and 0.428, with a range from 0.25 (GB-LCM-022 and GB-LCM-087) to 0.83 (GB-LCM-167) and from0.24 (GB-LCM-022 and GB-LCM-087) to 0.81 (GB-LCM-167), respectively. Five markers out of 10 markers, GB-LCM-022, GB-LCM-075, GB-LCM-104, GB-LCM-167 and GB-LCM-217, were selected as key markers for discrimination inboxthorn cultivars. All of boxthorn cultivars were individually distinguished by the combination of five SSR markers.