Ommatissus lybicus de Bergevin (Hemiptera: Tropiduchidae) is a key pest of date palm (Phoenix dactylifera Linnaeus; Arecaceae) with worldwide distribution and various management strategies. To study genetic diversity of date palm hopper, a series of experiments was conducted on genetic structure and genetic diversity of 15 geographic populations of O. lybicus (Abu Musa, Bam, Bushehr, Behbahan, Tezerj, Fin, Jiroft, Shahdad, Jahrom, Ghire Karzin, Ghasre Shirin, Iran; Pakistan; Oman; Egypt; and Tunisia) by amplified fragment length polymorphism, cytochrome c oxidase subunit I (COI), and 28S rRNA markers. Analysis of molecular variance analysis of amplified fragment length polymorphism data and COI sequences revealed a significant variation among O. lybicus populations (94.12% and 65.08% similarities for amplified fragment length polymorphism and COI, respectively). The 28S rDNA sequences from different populations were identical. Phylogenetic network inferred from amplified fragment length polymorphism data and COI sequences grouped two geographically close populations (Tezerj and Bam) in the two distinct clades while far apart geographical populations bunched in the same or close clades. These two populations experience repeated exposure to heavy pesticide applications annually. In conclusion, study of the genetic structure revealed a considerable variation between O. lybicus populations under intensive chemical strategies.