The study has established the F2 offspring oblained by crossing salt-tolerant alfalfa with salt-sensitive alfalfa, and the salt-tolerant F2 offspring seedlings was evaluated in a pot culture. With the F2 offspring, the study has obtained molecular marker linked with salt-tolerant genes of alfalfa by using the improved BSA and RAPD marker. The RAPD PCR products were recovered and purified using kit, then were sequenced. The DNA sequence was aligned in GenBank, the result of alignment showed that the DNA sequence was homological with one fragment (347 bp) of the mth2-6e18 of Medicago truncatula, and the similarity were 93%. mth2-6e18 is a molecular marker of cysteine proteases that plant salt inducible gene translated. It is extrapolated that this molecular marker has a significant correlation with cysteine proteases gene.