Abstract: In order to study the genetic diversity of different varieties of Stylosanthes guianensises, seven Stylosanthes guianensises were analyzed by AFLP and SSR markers. About 88 percent of 966 bands produced by using twelve AFLP primer combinations were polymorphic. The average polymorphic bands of each pair of primers were 70.8. 10 pairs of SSR primers generated 26 bands in which 21 bands were polymorphic. The range of the observed heterozygosity in 10 pairs of SSR primers was between 0 and 0.7143 with an average of 0.1857. The average of Shannon’s information index and the average content of polymorphism were 0.6545 and 0.727. Clustering tree was ploted based on UPGMA. The analysis results of AFLP and SSR markers were exactly similar. Seven Stylosanthes guianensises were divided into two groups. The genetic relationship between Stylosanthes humilis HBK and Stylosanthes scabra cv. Seca was the farthest and the genetic relationships between Stylosanthes guianensis cv. Oxley and Stylosanthes guianensis cv. Endeavour, Stylosanthes guianensis cv. Graham and Stylosanthes guianensis cv. Reyan No.5 were the closest.