Cold tolerance of 419 accessions of primary rice core collection from Guangxi was evaluated at geminating and seedling stages. The results indicated that the cold tolerance at geminating and seedling stages mainly concentrated in grade-7 and 9, most of the accessions were sensitive to cold. 24 and 27 accessions were classed into the high-level tolerance (Grade 1) at germinating and seeding stage, accounting for 5.73% and 6.44% of the total accessions, respectively. There is highly positive correlation (r = 0.66) between the cold tolerance scores at two stages. There were significant differences of cold tolerance between Indica and Japonica, non-glutinous rice and glutinous rice. Cold tolerance of Japonica was significantly higher than Indica at geminating and seedling stages. Cold tolerance of glutinous rice was significantly higher than non-glutinous rice at the geminating stage, but no difference at seedling stages. The rice collected from alpine areas showed much higher cold tolerance than Guinan and Guibei rice regions, no difference with Guizhong rice regions. Correlation analysis was carried on using 34 SSR markers. Two loci, at 7th and 9th chromosome, respectively , were identified to have a correlation with cold tolerance at both geminating and seedling stages. The study will provide elite rice germplasm of cold tolerance and a basis for mapping and cloning cold tolerance in rice.