This research was conducted in two main techniques: The first was Molecular genetic identification for twelve guava seedling trees. RAPD and ISSR based on PCR techniques five primers were used had successfully generated reproducible polymorphic products to study the genetic variability between the twelve guava seedling trees. Data cleared that, a total bands of guava seedling trees with RAPD - ISSR primers were recorded 94 band where the total polymorphic bands was recorded 48 with polymorphic percentage 51.06%. While, combining RAPD and ISSR, construct classify twelve guava seedling trees. Results from this analysis showed two main groups. The first main group was between seedling trees 9 and 12 and the second main group was divided into two sub main groups: the first sub main group included genotype 1 alone and the second sub main group was divided into two sub sub group which included the remained seedling trees. The second was: Protein electrophoresis analysis for the twelve guava seedling trees revealed a total number of 16 bands eight of them were polymorphic with 50% polymorphism. While, peroxidase and polyphenyl Oxidase analysis for the twelve guava seedling trees, all of bands illustrated were characterized for all the guava seedling trees studied, which all of them (monomorphic) with differences in their banding patterns densities