[Objectives] To investigate the molecular mechanism of gene differential expression in A.tuberosum under Botrytis cinerea stress. [Methods] The leaf of A. tuberosum was inoculated with B. cinerea to induce resistance, then leaf samples were taken at 2, 4, 8, 12 and 24 h, respectively, after inoculation, and used for cDNA-SCoT analysis to detect the gene differential expressions. [Results] More than 800 bands with length of 100–1800 bp were obtained using 60 SCoT primers. A total of 40 differentially expressed EST sequences were screened out, and 18 non-redundant ESTs with high quality were obtained by cluster analyses of the ESTs sequencing. The results of BlastN showed that the differential genes of A. tuberosum mainly related to disease defense, signal transduction, and protein metabolism. [Conclusions] Further analysis of gene function indicated that brassinosteroid biosynthesis-like proteins, NBS-LRR type disease resistance protein, jasmonic acid induced protein, abscisic stress ripening protein may be involved in the process of the incompatible interaction between the A. tuberosum and B. cinerea.