Leafhoppers are one of the most important agricultural insect pests. Traditional morphological criterion for leafhoppers identification depending on the presence of males only. So, Inter Simple Sequence Repeats (ISSRs) were used to find diagnostic markers for fingerprinting fifteen leafhoppers species collected from different medicinal and aromatic plants in Egypt. Seven ISSRs primers were successfully produced 72 bands those could be used to differentiate the fifteen different leafhopper species. Also different amplified bands with 65 diagnostic morphological characters were used to determine the phylogenetic relationship among the different species; that divided into two main clusters. ISSR-PCR technique could be successfully used with morphological characters to fingerprint and identify these leafhopper species using any life stage