Seven plant samples were collected from some locations of Syrian juniper (Juniperus drupacea Labill.) in Syria for molecular characterization and to determine the genetic relationships between them using ISSR technique (Inter Simple Sequence Repeats). Twenty three ISSR primers were used for this purpose, twelve primers showed polymorphism between studied samples and gave 89 bands, with polymorphism percentage of 95.5%. The band number resulted from each primer ranged between 4 bands for primers ISSR5 and ISSR9, and 12 bands for the primer ISSR1, with an average of 7.42 bands per primer. The minimum polymorphic percentage was 25% for primer ISSR9, and the maximum polymorphic percentage was 100% for the all primers except the primer ISSR9. The study showed correlation between the genetically converged samples and the collection sites (geographic correlation), the highest genetic relationship (93%) was within Latakia samples (Komat Alnabi Yonis – Jobet Bergal) and the lowest genetic relationship (42%) was between samples from Hamah (Jeb Alahmer) and Latakia (Almakamat) which refers to high genetic variation. The cluster analysis showed that the samples from nearby locations were gathered.