Coriander, Coriandrum sativum L., is an important medicinal plant belonging to the Apiaceae family, which is grown in many parts of Turkey. In this study, seven Turkish coriander varieties (Antakya, Arslan, Erbaa, Gurbuz, Kerkuk, Kudret-K, and Pelmus) were examined for phylogenetic relations using two ITS region (ITS4–ITS5) sequence information and their secondary structure analysis. The length of the nrDNA ITS sequences obtained in this study varied between 677 and 692 nucleotides for seven samples. The G + C content of the nrDNA ITS region ranged between 47.86 (ITS4) and 48.67% (ITS5). Secondary structural analysis revealed that variation between varieties is more unique. The AMOVA study confirmed the effectiveness of configuration analysis as variants accounted for the majority of the variance. In addition, variation within cultivars was significant (97%). This shows that a significant part of the variance detected in this study occurred among genotypes. Data analysis, including Shannon information index and scaled diversity overlap graph annotation, also showed that the highest level of heterozygosity occurred in the Arslan, Erbaa and Kudret-K genotypes, with cultivars showing more pronounced differences genotypically rather than geographically, consistent with the expected heterozygosity (80%). By verification of the PCoA analysis, the genotypes of Gurbuz and Arslan are very different from those of other groups. This supports the results of the cluster analysis, which showed that the Ankara-origin Gurbuz variety had a very different genotypic difference. Our analysis recommends the use of ITS4 sequence and secondary structure data at the intraspecific levels of coriander taxonomical classification. For the first time, a study has used both sequence information and secondary structural information to describe coriander at the varietal level of taxonomic classification.