Abstract: The purpose of this study focused on molecular mechanism in low temperature of watermelon seeding，making homologous diploid and triploid of watermelon of female precocious Jingxin as materials，using MSAP and cDNA-AFLP analysis of genes differentially expressed before and after low temperature stress，and selected different bands to be cloned，sequenced and compared. A total of 2 356 locus were amplied after using 28 MSAP primer combinations. Levels of decline in the total methylation were 8.5% and 10.4% of the diploid and the triploid of watermelon，respectively. Took 13 different bands with watermelon genome database，identified 7 bands as watermelon genome sequence. After being screened with 26 cDNA-AFLP primer combinations，1 267 bands were amplied：48.2% with up-regulatedexpression，51.8% with down-regulated expression in the diploid of watermelon；51.3% with up-regulated expression，48.7% with down-regulated expression in the triploid of watermelon. NCBI Blast search showed that 21 bands were homologous to functional genes，including hypothetical protein（38.1%），energy and metabolism protein（38.1%），signal transduction protein（9.5%），material transportation protein（9.5%），and DNA modification gene（4.8%），the function of the other 9 bands remained unknown. Under low temperature stress，the demethylation rate and up-regulated genes of the triploid of watermelon were greater than the diploid of watermelon，the triploid of watermelon induced more genes involved in energy and metabolism，signal transduction and transportation process，illustrating that the triploid of watermelon had stronger resistance to low temperature than the diploid of watermelon.

Key words: watermelon, cold stress, MSAP, cDNA-AFLP, gene expression