The molecular characterization of C. sativus accessions is of great interest for clonal selection and preservation of valuable resources with the best productive traits and specific patterns related to local products. To analyze the genetic diversity of Moroccan saffron, fourteen new saffron accessions were evaluated, twelve of which were from Morocco and two from Kozani in Greece, and the Quercy region of France. These accessions differ by their geographical distribution and altitudes. Seven specific C. sativus Simple-sequence repeats (SSRs) primers were considered. Their combinations generated 13 monomorphic alleles across all studied accessions with an average of 1.85 allele/locus. Additionally, fourteen unique ABRII/Cs30 SSR locus sequences were obtained and registered in the NCBI database (MZ868510-MZ868523). Single nucleotide polymorphism (SNP) was also assessed considering the ABRII/Cs30 locus. By excluding gaps and missing data from the sequence alignment, 161 sites were produced. The DnaSP analysis of all accessions revealed 40 polymorphic sites, including thirty-two among the Moroccan accessions. Nucleotide diversity (PiT) was 0.03896, while the average nucleotide difference was 6.27273. The haplotype diversity (HD) of Moroccan and all accessions was 0.848 and 0.875, respectively, demonstrating a strong capacity of the ABRII/Cs30 locus to distinguish saffron accessions. The Tazenakht (TK) population was the most polymorphic, while the Low land (TB) population was monomorphic. Sequence-based genetic relationships imply that Moroccan saffron likely originated from Greece. Our results show that the SNPs approach is a powerful tool to evaluate genetic diversity among C. sativus accessions. The present molecular analysis indicates that Moroccan saffron is not a single clone. This outcome constitutes a sound basis for developing a core collection representative of the biodiversity of Moroccan saffron to conserve and enhance this critical commodity.