To identify single nucleotide polymorphisms (SNPs) in eugenol O-methyl transferase (EOMT) and Chavicol O-methyl transferase (CVOMT) genes, cleaved amplified polymorphic sequence (CAPS) markers and direct sequencing were used in different basil populations. Fragments with sizes of 571 and 908 bp of coding regions of both genes were amplified and digested with restriction enzymes Pst1 and MseI. In silico digestion of the coding region of the genes by Pst1 produced fragments of 480 and 91 bp in EOMT and 621 and 287 bp in CVOMT. However, no polymorphic restricted patterns were produced in 80 basil individuals using Pst1 digestion. In silico MseI digestion of EOMT and CVOMT gene sequences produces fragments of 59, 135 and 377 bp, and 275, 302 and 331 bp, respectively. Digestion of the amplified fragments of both genes generated polymorphic banding patterns in studied basil genotypes. One out of each different restriction patters which is produced for both genes in basil genotypes, was selected for sequencing. Sequences obtained, were aligned for both genes using Clustal Omega and SNPs were identified. The results of EOMT alignment revealed transition mutations TC and AG, but no transversion was observed in this gene. Mutations AG, TC, AC and AT were found in CVOMT gene with the highest frequency of AG. In conclusion, the results of the current investigation revealed low polymorphism in coding regions of the studied genes and demonstrated the conservity of the coding regions of both genes during basil evolution.