Sunflower (Helianthus annuus L.) is one of the pioneer crops with extremely strong adaptability to adverse stresses, and its stress (such as high salinity) tolerance improvement will contribute to the utilization of abundant marginal land and promote sustainable development. However, the genetic determinants underlying response to salt stress are not fully understood. Here, we perform a genome-wide association study (GWAS) using 31 traits from a high-throughput platform in 342 oilseed sunflower accessions at the germination stage under salt stress conditions. We identify 359 significantly associated SNPs and 63 InDels corresponding to 424 and 83 candidate genes, respectively. One candidate gene, C-Repeat Binding Factor 4 (CBF4)—a member of the AP2/EREBP family transcription factor—directly binds to dehydration-responsive element in the promoter region of its downstream target gene, High-Affinity K+  transporter 11 (HAK11), thereby activating its expression. This regulatory mechanism contributes to enhanced salt tolerance in sunflower by modulating established salt-responsive genetic pathways. Collectively, our findings provide new insights into salt tolerance mechanisms and offer valuable genetic resources for breeding salt-tolerant sunflower cultivars.

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