Abstract: Qianban Lotus, is a special type of lotus in Nelumbo nucifera Gaertn., which stamen and pistil are completely transformed petals and more than one-thousand petals may be observed during all the period of flowering. To discover the genetic relationships among current cultivars, 5 cultivars from three regions in Yunnan province and one from Yuquan Temple, Dangyang, Hubei province were investigated by employing randomly amplified polymorphic DNA (RAPD) markers. The selected sixteen primers amplified 141 bands in total, of which 81 were polymorphic (57.45%). Our result also exhibited that these cultivars had obvious genetic differentiation with relatively distant genetic distance. There is relatively high level of genetic diversity among these cultivars. No significant genetic differentiation was observed between those cultivars from Yunnan and the one from Yuquan Temple. The cultivars from Yunnan province were found to have obvious genetic differentiation, and the Yaoan lotus displayed its unique genetic characteristics at the most.