Asexual reproduction is theorised to have detrimental consequences for genome function, such as the accumulation of deleterious mutations or disruptions to genome structure and gene expression. However, asexuality has evolved repeatedly in some animal taxa, challenging our understanding of its evolutionary impacts. Our project aims to investigate the genomic consequences of asexuality in the New Zealand stick insect genus Acanthoxyla. In this genus, hybridization between sexual ancestors have produced multiple asexual lineages that reproduce exclusively by parthenogenesis and form female-only populations. To investigate the genomic consequences of asexuality in Acanthoxyla, we (1) generated high-quality, haplotype-resolved reference genomes for four allopolyploid lineages, (2) performed comparative genomic analyses between the asexual lineages and one sexual relative, and (3) examined allele-specific expression and its potential regulation by epigenetic mechanisms within their hybrid genomes. Haplotype-resolved genome assemblies using Nanopore long reads, Illumina short reads and Hi-C data produced highly contiguous (scaffold N50: 300 Mb), duplicated (BUSCO: 96 %) and large (phased assembly size: 9.5-11 Gb) chromosome-level genomes for the four Acanthoxyla lineages. Using orthologs from distantly related sexual stick insects and a mapping-based approach, we identified the X and neo-X chromosomes in the Acanthoxyla genomes. Comparative analyses of the Acanthoxyla lineages revealed extensive structural rearrangements among hybrid subgenomes, while the X and neo-X chromosomes remained highly conserved across lineages. Ongoing analyses using RNA sequencing and Nanopore methylation data are investigating allele-specific expression and differential methylation, providing insight into potential epigenetic regulation of gene expression in these hybrids. Together, these high-quality genome assemblies and complementary analyses provide new insights on the genomic consequences of asexual reproduction and hybridization, while also providing genomic resources for New Zealand’s endemic stick insects.