BackgroundThe plant bug,Pachypeltis micranthusMu et Liu (Hemiptera: Miridae), is an effective potential biological control agent forMikania micranthaH.B.K. (Asteraceae; one of the most notorious invasive weeds worldwide). However, limited knowledge about this species hindered its practical application and research. Accordingly, sequencing the genome of this mirid bug holds great significance in controllingM. micrantha.ResultsHere, 712.72 Mb high-quality chromosome-level scaffolds ofP. micranthuswere generated, of which 707.51 Mb (99.27%) of assembled sequences were anchored onto 15 chromosome-level scaffolds with contig N50 of 16.84 Mb. TheP. micranthusgenome had the highest GC content (42.43%) and the second highest proportion of repetitive sequences (375.82 Mb, 52.73%) than the three other mirid bugs (i.e.,Apolygus lucorum,Cyrtorhinus lividipennis, andNesidiocoris tenuis). Phylogenetic analysis showed thatP. micranthusclustered with other mirid bugs and diverged from the common ancestor approximately 200 million years ago. Gene family expansion and/or contraction were analyzed, and significantly expanded gene families associated withP. micranthusfeeding and adaptation toM. micranthawere manually identified. Compared with the whole body, transcriptome analysis of the salivary gland revealed that most of the upregulated genes were significantly associated with metabolism pathways and peptidase activity, particularly among cysteine peptidase, serine peptidase, and polygalacturonase; this could be one of the reasons for precisely and highly efficient feeding by the oligophagous bugP. micranthusonM. micrantha.ConclusionCollectively, this work provides a crucial chromosome-level scaffolds resource to study the evolutionary adaptation between mirid bug and their host. It is also helpful in searching for novel environment-friendly biological strategies to controlM. micrantha.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09445-8.