Abstract: 【Objective】Isolation of differentially expressed genes induced by Puccinia striiformis is the first step to reveal the molecular mechanism of interaction between wheat and yellow rust fungus. 【Method】A SSH-cDNA library was constructed with wheat variety shuiyuan-11 and a Chinese virulent race CY31 of Puccinia striiformis, 250 positive clones were selected for sequencing.【Result】In total 149 nonredundant ESTs were assembled with CAP3, then function annotation and classification were performed. There were 50 unigenes (33.6%) without or with weak similarities to the existent proteins in the nr database from NCBI and 25 unigenes (16.8%) significantly matched with hypothetical protein. Whilst the unigenes assigned to primary metabolism, energy and disease/defence accounted for 8.7%, 6.7%, 4.0%, respectively. Only 2 unigenes, however, had higher similarity with pathogenic protein. Four genes were randomly selected to investigate their expression profiles by reverse transcription PCR (RT-PCR). 【Conclusion】Some genes which had higher similarity with catalase, elongation factor and cell death suppressor protein were supposed to have important roles during compatible interaction between Puccinia striiformis and wheat.