The objective of this study was to characterize and determine the genetic variation among twelve cultivars and four rootstocks, belonging to Amygdalus genus in Syria using the simple sequence repeats (SSRs) marker. It was found that 154 alleles were identified by using 26 primer pairs, and the proportion of the specific ones was 30.52%. In addition, it was revealed that all the studied SSR loci produced polymorphic alleles. The average of PIC, He and Ho were 0.58, 0.61, 0.31, respectively.