The study was executed during two successive years (2016 and 2017) in the Orchard of Deciduous fruit department and Biotechnology Research lab of Horticulture Research Institute, Agriculture Research Center, Giza, Egypt. The aim of the work was using one year old plants of five and four seedy strains of Pear (Betulaefolia) and Peach (Mit-Ghamr) deciduous fruit rootstocks, where the study carried out to evaluate the molecular genetic variability between the two seedy strains rootstock respectively by using two molecular genetic markers, ISSR and SCoT based on PCR techniques to support the use of marker-assisted selection (MAS) for detection of a biotic and biotic stress in seedy strains.
      Six and Ten primers were used with ISSR and SCoT molecular genetic markers had successfully generated reproducible polymorphic products to study the genetic variability between Betulaefolia and Mit-Ghamr rootstocks. Data cleared that high levels of polymorphism among the strains studied of each rootstock,wherea total bands of five seedy strains of Betulaefolia rootstock with   ISSR- SCoT primers were recorded 105 band (43-62 respectively), and the total monomorphic bands were 29 (11-18) added to total polymorphic bands was recorded 76 (32-44) with polymorphic percentage (74.44% - 71%) where the specific marker bands were 30 (13 -17) respectively. On the other hand, four seedy strains of Mit-Ghamr rootstock with ISSR- SCoT primers data recorded 97 total bands as (31-66 respectively).