Abstract: In order to screen out molecular markers suitable for the genetic diversity of cured tobacco leaves, the polymorphism and stability of SRAP and SSR markers in cured tobacco leaves were detected by capillary electrophoresis. The genetic diversities of 9 flue-cured tobacco cultivars, including Yunyan 87, Yunyan 97, Yunyan 116, Cuibi 1, Honghuadajinyuan, Zhongyan 100, K326, KRK26 and NC297, were analyzed based on SSR marker with good stability. The results showed that the DNA degradation of cured tobacco leaves was more serious than fresh tobacco leaves, and the degradation mainly occurred in the middle and late periods of stem-drying stage. Compared with SRAP markers, SSR markers had better amplification stability in cured tobacco leaves, while their polymorphisms were slightly worse. In addition, eight pairs of SSR primers such as NTGS66290, NTGS66292, NTGS66295, PT30008, PT30169, PT30361, PT30403 and PT30424 can effectively distinguish 9 flue-cured tobacco varieties. The genetic similarity coefficients were from 0.250 to 0.900 with the average value of 0.622.