The codling moth, Cydia pomonella (Lepidoptera, Tortricidae), is a wide-spread and highly impactful pest of pome fruits (apple and pear) and walnut. We sequenced the genome of this pest by using a combined strategy of Illunima HiSeq2000, PacBio, BioNano and HiC scaffolding, we identified 27 autosome, Z and W chromosome. The gene annotation was carried out using the OMIGA pipeline. Please feel free to contact us for any question: Professor Fei Li, lifei18@zju.edu.cn.