In this study, we assembled the chromosome-scale genome sequence of K. pelamis utilizing a combination of PacBio long reads and Hi-C technology. The initial assembly spanned 1,612 Mb across 845 contigs with a contig N50 of 9.4 Mb. Following redundancy removal and Hi-C scaffolding, totaling 836.42 Mb, was anchored to 24 pseudo-chromosomes, yielding a scaffold N50 of 32.7 Mb with 390 scaffolds. Annotation revealed 218.52 Mb of repetitive sequences, predominantly consisting of DNA transposons (53.92 Mb, 6.44%) and LINEs (21.46 Mb, 2.56%). A total of 32,001 protein-coding genes were predicted using a combined approach of homology-based, transcriptome-based, ab initio methods, with 31,993 genes (99.98%) annotated. Upon conducting BUSCO analysis with the Actinopterygii_odb10 database, the results included 3,591 (98.7%) complete BUSCOs, 3,523 (96.8%) single-copy BUSCOs, 68 (1.9%) duplicated BUSCOs, 19 (0.5%) fragmented BUSCOs, and 30 (0.8%) missing BUSCOs.