The genus Helopeltis (Hemiptera: Miridae) includes some of the major pests of cashew (Anacardium occidentale L. [Anacardiaceae]). Helopeltis species severely damage tender shoots, inflorescences, immature cashew nuts and associated cashew apples (pseudocarps). In India cashew crop losses of more than 40% caused by Helopeltis species are often reported. One of the major limitations in meeting this problem has been the lack of taxonomic knowledge of the Helopeltis species complex, its distribution, host range, and the associated parasitoid complex. The two major pests of cashew, Helopeltis antonii and Helopeltis theivora closely resemble each other. Morphological identification of these species can be facilitated by the use of DNA barcoding of the mitochondrial cytochrome C oxidase subunit 1 (COX-1) and the development of species-specific molecular markers; and we accomplished both of these objectives in this study. These molecular markers also enable non-specialists to identify the above mentioned species in their various life stages, i.e., egg, nymph and adult. The molecular identification of H. antonii and H. theivora has been corroborated with morphological identification. We examined genetic differences in COX-1 sequences among 12 populations of H. antonii collected from different geographic locations in India for the first time. The phylogenetic analysis did not show any geographic or host-associated genetic differences in H. antonii, which were collected on different host plants. The present investigation resulted in the development of molecular technology to achieve quick, accurate and timely identification of H. antonii and H. theivora, a critical factor in understanding the epidemiology of the crop losses in cashew, resistance management and also in quarantine.