SRAP and SSR analysis were performed on 20 main black sesame cultivars released in China with 23 pairs of primers for analyzing genetic diversity. The results showed that: A total of 672 DNA bands were amplified by 23 pairs of SRAP primers, with 152 of them were polymorphic, resulting polymorphic ratio of 22.26%, and the total and polymorphic bands amplified by every primer pair averaged 29.21 and 6.61, respectively. In SSR, 92 DNA bands were amplified by 23 polymorphic primer pairs, each primer amplified 3-6 total bands and 1-5 polymorphic bands, the average was 4.00 and 3.09, respectively, and the degree of polymorphic bands was 77.17% averagely. Genetic similarity and genetic distance of 20 black sesame cultivars were 0.8547-0.9804 and 0.0159-0.0921, indicating limited genetic diversity and narrow genetic basis. The clustering results showed that 11 cultivars from main producing area Jiangxi were obviously clustered together, and the genetic similarity of Jiangxi black sesame cultivars was higher than that of the cultivars in other provinces, with the genetic distance lower than other province and the differences of them all reached a very significant level. Strengthening the introduction and utilization of germplasm is an urgent need for broadening the genetic basis of black sesame cultivars in China.