Among molecular markers, simple sequence repeat (SSR) has become established as an excellent tool for studying genetic diversity due to several desirable attributes including abundance, its multiallelic and codominant nature, high level of reproducibility and cross-species transferability (Gupta et al., 1996; Gupta and Varshney, 2000). An SSR marker has been shown to be almost twice as informative as an random-amplified polymorphic DNA (RAPD) marker and much more informative than restriction fragment length polymorphism in soybean (Powell et al., 1996). On the other hand, amplified fragment length polymorphism (AFLP) is a high multiplex polymerase chain reaction (PCR)-based dominant marker (Vos et al., 1995). It has the potential to generate large numbers of polymorphic loci (Powell et al., 1996).