The critically endangered hawksbill turtle (Eretmochelys imbricata) is a species of significant ecological and conservation importance. This study presents a comprehensive genomic analysis of E. imbricata, combining high-quality genome sequencing with population genetics in the South China Sea. We report the first chromosome-level genome assembly for E. imbricata, spanning 2,138.26 Mb with a contig N50 of 123.49 Mb and scaffold N50 of 137.21 Mb. The assembly comprises 28 chromosomes containing 20,206 protein-coding genes, with 99.48% functionally annotated. Comparative genomic analysis revealed an expansion in olfactory receptor genes and positive selection in immune, sensory, and aging-related systems, suggesting adaptations to aquatic environments and longevity. We further investigated the genetic structure of hawksbill turtle populations in Naozhou Island Waters using whole-genome resequencing of 13 individuals. The analysis yielded 337.54 GB of high-quality data with an average sequencing depth of 11x. We identified 12,703,462 SNPs, with 114,273 located in exonic regions. PCA analysis showed no distinct clustering, indicating diverse origins of the sampled individuals. Demographic analysis revealed population fluctuations over the past 50 million years, with a recent sharp decline stabilizing around 1 million years ago. LD analysis indicated high genetic diversity, particularly on chromosomes 1, 13, 14, and 24—annotation of polymorphic sites highlighted olfactory receptor and immunoglobulin heavy chain genes under strong positive selection.

Hawksbill turtle,Eretmochelys imbricata,Genome,SNP,D-loop