In order to explore the correlation between cysteine proteases and the senescence of determinate nodules,LjCyp1 and LjCyp5,associated with root nodule senescence were identified from Lotus japonicus by sequence alignment analysis with cysteine protease AsNODf32.The protein sequence and structure showed that the homology of LjCyp1 and LjCyp5 was as high as 96.2%,both of which contained two typical cysteine protease domains and vacuolar localization signal peptides,belonging to the papain family. In vitro enzyme activity assays showed that both proteins had cysteine protease activity. Realtime PCR and histochemical localization analysis showed that two protease genes were mainly expressed in mature and aged root nodules. The results indicated that LjCyp1 and LjCyp5 cysteine proteases may play an important role during nodule senescence in Lotus japonicus.