Abstract: 36 Phalaenopsis cultivars’s the genetic diversities and the genetic relationships were analyzed by using molecular marker technique of inter-simple sequence repeat (ISSR). The results showed 11 primers selected out of 100 primers amplfied 98 reproducible DNA bands, of which 91 bands were demonstrated polymorphism, and the polymorphic rate was 92.86%. The similarity coefficient between the cultivars ranged 0.57-0.96, showing that there was rich genetic diversity among the cultivars. Moreover, 4 specific ISSR bands were obtained, which could be used to identify 3 varieties of Phalaenopsis tested. 36 varieties could be divided into 7 groups at the genetic distance of L=0.644. Among them, the 3 largest groups represented yellow, white and red, respectively, while in the same color relationships, the groups were separated by the lip color, which showed the result of clustering analysis was generally consistent with color.