Acacia tortilis is a medium to large canopied tree, widely planted in desert regions of Hormozgan province in Iran. It is considered one of the most important species for reforestation of arid areas and to reduce desertification. To protect the trees against pests and diseases, a comprehensive and ecofriendly control plan is required. In recent years, a stinkbug species was observed on A. tortilis. It severely damages the trees by feeding on sap and producing honeydew that promotes sooty mold growth. The aim of the present study was to identify this stinkbug pest to species level and characterize its bacterial endosymbiont fauna with a view to designing a control program. Phylogenetic analyses using a partial COI gene sequence indicated that Nysius cymoides was the pest species damaging the trees. Sequencing of 16S rRNA and wsp showed that N. cymoides harbors two obligate endo symbionts: “Candidatus Schneideria nysicola” and “Candidatus Sulcia muelleri” and three facultative endosymbionts: Wolbachia, Pantoea, and Enterobacter. This work is the first report of Nysius cymoides as a serious pest on Acacia tortilis as well as the first characterization of its bacterial endosymbiont fauna.