Protein hydrolyzation is activated and involved in response to various stress signals. In the present study, a full-length cDNA, named MsCP1, encoding a papain-like cysteine protease was obtained by degenerated primers and 3'- and 5'-RACE from salt-tolerant alfalfa. The cDNA contained an open reading frame encoding a deduced protein of 350 amino acids with a putative N-terminal signal peptide, NPIR vacuole-sorting signal sequence and potential N-linked glycosylation sites. The deduced sequence showed a high similarity to deduced proteins from pea, tobacco, tomato and ryegrass. Fusion expression analysis in Escherichia coli showed that the putative eukaryotic signal peptide prevented its expression in prokaryotic system. The integration and transcript of the expression elements in transgenic tobacco plants were detected with Southern blot and RT-PCR analysis.