Abstract: In this study，the low semi-lethal temperature（LT50）was investigated for leaves at rhizome stage（RS），budding stage（RS），and flowering stage（FS），and ray florets at flowering stage（RFS）of 58 cut chrysanthemum accessions，and elite alleles and candidate genes relevant to cold tolerance were examined using genome-wide association analysis. The results showed that，the cold tolerance varied widely for leaves at different stages and ray florets at the flowering stage in the investigated cut chrysanthemums，with coefficients of variation larger than 25%. Statistical analysis by the additive main effects and multiplicative interaction effects（AMMI）model revealed that several accessions showed stronger cold tolerance and expressed stably across different stages. The genome-wide association analysis based on 36 737 high-quality SNPs and mixed linear model（MLM）identified a total of 24 SNPs that are significantly associated with cold tolerance，each five for RS and FS，11 for BS，and three for RFS. Among which，five SNPs showing a phenotypic effect <–4 ℃ should be elite alleles for cold tolerance. Blasting the SLAF tags harboring the cold tolerance-associated SNPs with the transcriptomes of chrysanthemum，CL2042.Contig4_All and Unigene40993_All might function in tolerance to cold stress.

Key words: chrysanthemum, cold tolerance, genome-wide association analysis, candidate genes