[Objectives]  To analyze genome-level species differences between two sibling species of tea geometrids, Ectropis grisescens and E. obliqua, two major lepidopteran pests in southeast Asian tea plantations with very similar morphology, but different susceptibility to the E. obliqua nuclear polyhedrosis virus (EoNPV), a common biological pesticide. [Methods]  We assembled and annotated the draft genomes of E. grisescens and E. obliqua by whole-genome sequencing data and conducted comparative genomic analysis. Flow cytometry was used to estimate the genome size of each species, after which low-coverage genome sequencing data were obtained using Illumina next-generation sequencing technology. After genome assembly and annotation, we conducted phylogenetic and synteny analysis. Positive selection analysis of 1 018 single-copy homologous genes was also conducted. We then analyzed chemosensory genes and those involved in EoNPV resistance and identified and verified species-specific sequences. [Results]  We used low-coverage genome survey sequencing to successfully assemble and annotate the draft genomes of E. grisescens and E. obliqua, which have a similar genome size of 770 megabase (Mb) pairs. Comparative genomics indicates a similar length of contigs, scaffolds and gene number, but a different number of repeat sequences (52.62% for E. grisescens and 49.67% for E. obliqua). Phylogenetic and whole-genome synteny analysis indicates that these sibling species diverged 318 million year ago with no obvious chromosome rearrangement. Gene expansion of apolipophorin and cathepsin has occurred, including significant positive selection on the GO pathway 0044281 (small molecule metabolic process) in E. grisescens. [Conclusion]  We successfully used genome survey sequencing to assemble and annotate draft genomes of E. grisescens and E. obliqua. The results provide fundamental data for genetic comparison between these tea geometrids, thereby facilitating understanding of the adaptive evolution of sibling species, and may also allow reduced pesticide use and promote more environmentally friendly methods of controlling these pests.