Shami goat in Syria is one of the important domestic breeds, because of its high productivity and breeding capacity under the hard environmental conditions and it is still being used in crossbreeding with Mountain goats as a donor for milk producing traits. This breed is still far away from scientific investigations even it has been exposed to a random crossbreeding with Mountain goats by goat breeders. This has lead to the possibility of losing some of its genetic characteristics which are not detected yet. In this research the genetic diversity among groups of pure Shami goats was determined using ISSR-PCR on blood and results indicated that there was a molecular genetic diversity among studied goats and polymorphic rate was register to 100%.