Abstract
Background Comstockaspis perniciosa (Comstock, 1881) is one of the most destructive quarantine pests of fruit crops, posing a serious threat to commercial orchards and natural populations of wild apple trees. Despite its widespread distribution, information on the molecular genetic characteristics of this species in Central Asia remains limited. Methods The aim of this study was to characterize C. perniciosa collected from commercial orchards in southeastern Kazakhstan based on external morphological observations and molecular data, determine the phylogenetic position of the examined specimens using 28S rRNA gene sequences, and detect associated parasitoids using high-throughput sequencing technologies. During the growing season in 2025, surveys were conducted in ten commercial orchards, including sites located near natural populations of wild apple trees. Results Species-level identification of the collected specimens was confirmed by analysis of the 28S rRNA gene. All sequences clustered with reference C. perniciosa sequences, confirming species identity. Analysis of the high-throughput sequencing data additionally revealed sequences of parasitoids belonging to the genus Aphytis (Hymenoptera: Aphelinidae) in ten samples, indicating the presence of natural enemies associated with C. perniciosa . Conclusions These findings expand current knowledge of the molecular characteristics of C. perniciosa in Central Asia and demonstrate the potential of NGS (Next Generation Sequencing) technologies for the simultaneous detection of quarantine pests and their associated entomophagous natural enemies within phytosanitary monitoring programs.