Aphids are considered as most economically importance and worldwide insect pests. Successful pest management systems are based on accurate and rapid pests' species identification. Traditional morphological identification of closed aphid species may be considered as inaccurate taxonomic process. For overcoming disadvantages of traditional morphological identification, molecular techniques, related to DNA markers and based on polymerase chain reaction (PCR), were approached by using nine ISSRs primers to identify and diagnose fifteen common aphid species that disperse in Egyptian agro-ecosystem. The examined ISSRs primers could successfully discriminate the tested aphid species that reflected 61.39% polymorphism among them. Moreover, four banding patterns were considered as unique bands which could characterize three aphid species (Aphis gossypii, Aphis nerii and Myzus persicae). Highest genetic homology (84.9%) was observed between species Rhopalosipum padi and Schizaphis graminum. In additions, each of A. gossypii and Aphis citricola were also genetically homologous species. In contrast, species Aphis craccivora and M. persicae were analogous genetically with low similarity percentile (59.8%). High genetic divergence was observed also between A. nerii and M. persicae. Two alternative molecular branching taxonomic keys were proposed by subjecting five highest polymorphic ISSRs primers and 29 banding patterns with different molecular sizes.