Abstract: Cold tolerance at the seedling stage(CTS) are one of important factors affecting the development of growth in rice. In this study, we analyzed and located quantitative trait loci (QTL) for cold tolerance to cold tolerance at the seedling stage (CTS) using a backcross inbred lines (BILs) derived from a backcross of Koshihikari(japonica)/Kasalath(indica)//Koshihikari through 162 RFLP markers. Resultantly, continuous phenotypic variations for CTS was observed, indicating that CTS was quantitatively inherited traits. Four QTLs for CTS were located on chromosome 1、3、11、12 , which explained 7.4%-21.9% of the phenotypic variance, respectively, all alleles increasing CTS come from the Koshihikari parent. Through fine mapping, a major QTL(qCTS-12) on chromosome 12 was narrowed to the physical distance of 77kb between RM28596 and R1709. These results and molecular markers tightly linked to QTLs detected in this study can provide useful information for molecular breeding and cloning of of cold tolerance genes in rice.