Moths and butterflies (Lepidoptera) have a heterogametic sex chromosome system with females carrying ZW chromosomes and males ZZ. The lack of W chromosomes in early diverging lepidopteran lineages has led to the suggestion of an ancestral Z0 system in this clade and a B chromosome origin of the W. This contrasts with the canonical model of W chromosome evolution in which the W would have originated from the same homologous autosomal pair as the Z chromosome. Despite the distinct models proposed, the rapid evolution of the W chromosome has hindered the elucidation of its origin. Here, we present high-quality, chromosome-level genome assemblies of two Hypolimnas species (Hypolimnas bolina and Hypolimnas misippus) and use the H. misippus assembly to explore the evolution of W chromosomes in butterflies and moths. We show that in H. misippus the W chromosome has higher similarity to the Z chromosome than any other chromosome, which could suggest a possible origin from the same homologous autosome pair as the Z chromosome. However, using genome assemblies of closely related species (ditrysian lineages) containing assembled W chromosomes, we present contrasting evidence suggesting that the W chromosome might have evolved from a B chromosome instead. Crucially, by using a synteny analysis to infer homology, we show that W chromosomes are likely to share a common evolutionary origin in Lepidoptera. This study highlights the difficulty of studying the evolution of W chromosomes and contributes to better understanding its evolutionary origins. Supplementary data for The Hypolimnas misippus genome supports a common origin of the W chromosome in Lepidoptera Anna Orteu, Shane A. McCarthy, Emily A. Hornett, Mathew Gemmel, Louise A. Reynolds, Ian A. Warren, Ian J. Gordon, Gregory D. D. Hurst, Richard Durbin, Simon H. Martin, Chris D. Jiggins bioRxiv 2023.03.24.533969; doi: https://doi.org/10.1101/2023.03.24.533969 Files: Hbol_pilonPolished_augustus.hints_utr.gtf- Hypolimnas bolina genome annotation Hmis_augustus.hints_utr.gtf- Hypolimnas misippus genome annotation map_GCA_905220365.1_ilVanCard2.1_genomic_to_ilHypMisi1.trio.hap2.p_ctg.purge.FINAL.paf- Minimap2 alignment of Hypolimnas misippus and Vanessa cardui genomes map_Junonia_coenia_Jc_v2.scaffolds_to_ilHypMisi1.trio.hap2.p_ctg.purge.FINAL.paf- Minimap2 alignment of Hypolimnas misippus and Junonia coenia genomes Annotation_stats_ncbi_dataset.tsv- A dataset containing statistics on publicly available annotations of Lepidoptera genome assemblies Hmis_interproscan.tsv- InterProScan results of the HypMis_v2 annotation Hbol_interproscan.tsv- InterProScan results of the HypBol_v1 annotation Hmis_interproscan_transposable_elements.tsv- InterProScan results of transposable element related genes in the HypMis_v2 annotation Hbol_interproscan_transposable_elements.tsv- InterProScan results of transposable element related genes in the HypBol_v1 annotation