Nine polymorphic primer pairs were developed from 8,188 ESTs of Phalaenopsis from NCBI and used to analysis genetic diversity of 16 common Phalaenopsis materials on the market. The results indicated that 45 alleles loci were detected across 9 EST-SSR loci. The average number of alleles per EST-SSR locus was 5 with a range from 2 to 12. The value of allelic polymorphism information content (PIC) ranged from 0.527 to 0.981, on an average of 0.755 per EST-SSR marker. The genetic similarity of paired varieties ranged from 0.550 to 0.875, with average 0.728. The results showed that the commom Phalaenopsis varieties on the market had closer genetic relationgship with each other. Cluster analysis based on the UPGMA method indicated that the 16 Phalaenopsis varieties could be divided into four groups at similarities coefficient of 0.73, which was generally consistent with color. The Group Ⅰ included ten cultivars, such as Dtps. Queen Beer ‘Red Sky’, Dtps. Jiuhbao Red Rose, et al. The Group Ⅱ included four cultivars, such as P. Taida Salu, P. Fuller’s Sunset, Dtps. Chain Xen Queen, Dtps. Shin-yaun Golden Beauty. The Group Ⅲ included one cultivar P. Brother Sara Gold. The Group Ⅳ included one cultivar P. amabilis cv. Formosum. The results of the study will provide referrence for Phalaenopsis cultivar breeding.