<p>Safflower (<i>Carthamus tinctorius</i> L.) is an underutilized oilseed crop, primarly cultivated for its seed oil content and has significant economic potential. Despite its historical significance, safflower remains an orphan crop with limited genetic improvement and genomic resources. In this study, the genetic diversity and population structure of 184 safflower accessions from the Indian National Gene Bank were assessed using 18 simple sequence repeats (SSR) and 7379 single-nucleotide polymorphisms (SNP). Our analysis revealed high polymorphism in both marker system, with SSR markers exhibiting high polymorphism (95%) and gene diversity (0.96), with an average of 44 alleles per marker. The SNP markers showed an average gene diversity of 0.41 and a polymorphic information content of 0.32. Population structure analysis using SSR markers revealed three clusters, whereas SNP markers identified two clusters. Principal coordinate analysis (PCoA) using SNP markers displayed clear differentiation between the two populations and the admixture, whereas SSR markers showed no significant differences. Analysis of molecular variance (AMOVA) revealed 2% and 3% variance among populations using SSR and SNP markers, respectively. The results suggest that SNP markers are more effective than SSR markers in delineating population structure in safflower. This study provides valuable insights into the genetic diversity and population structure of the safflower germplasm, which can be utilized for the effective management of plant genetic resources and crop improvement programs.</p>