Cereal aphids are one of the most important insect pests limiting cereal production worldwide. Classical morphological criteria for aphid species identification may be affected by environmental factors such as climatic conditions and physiological status of the host plant. So, two modern molecular techniques; Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSRs) were used to find diagnostic markers for fingerprinting eleven cereal aphids those collected from different cereal plants and from different localities in Egypt. Eight RAPD and five ISSRs primers were successfully produced 97 and 69 markers that could be used to differentiate the eleven different cereal aphid species. Also these molecular techniques with 23 diagnostic morphological characters were used to find the Phylogenetic relationship among the different collected species; that divided into two clusters with similarity matrix percentages of 73 and 82%. From these results it could concluded that these techniques could be successfully used successively to fingerprint and identify these aphid species and differentiate among them.