Almond is an economically important plant with a high genetic diversity, therefore molecular methods are reliable approaches to define and verify rapidly and correctly such diversity. This research sought the use of molecular markers for identifying and barcoding Almond genotypes in Duhok Province KRG- Iraq. It involved the application of Internal Transcribed Spacer region,18S-28S intergenic spacers, sequencing and Single Nucleotide Polymorphism identification. For this study, 8 genotypes were collected from various regions, namely the Barwari, Zakho, Bajlor, Kora, Kemeka, Pirumara, Qirqrava and Deragzhnic. The PCR amplification products of the ITS region and 18S–28S rDNA intergenic spacer were 700 bp. and 850 bp. respectively. To determine the types and the number of SNPs in the different genotypes, the sequencing data obtained in this study were compared to those in the NCBI. The SNPs results in the ITS region revealed 6 transversions within the Bajlor genotype (sequence three) and the clustering analysis showed that the eight almond genotypes were grouped into three main groups. Whereas SNPs results in the 18S–28S rDNA intergenic spacer detected a total number of 38 positions. 16 transition and 22 transversion sites within the Bajlor genotype (sequence three) while clustering analysis showed that the eight almond genotypes were grouped into two main groups. This study showed the feasibility of using those markers for possible DNA barcoding and identification of Almond genotypes in this region.