Marsupenaeus japonicus is an important marine crustacean species. However, a lack of genomic resources hinders the use of whole genome sequencing to explore their genetic basis and molecular mechanisms for genome-assisted breeding. Consequently, we determined the chromosome-level genome of M. japonicus. In total, 478.42 Gb of genomic sequencing data were obtained using the PacBio platform. A final genome assembly of 1.54 Gb was generated with a contig N50 of 229.97 kb. The 266 Contigs were categorized into 42 chromosomes using high‐throughput chromosome conformation capture (Hi-C) technology, with a scaffold N50 of 38.27 Mb, occupying 95.9% of the genome. We identified 24,317 protein-coding genes in the M. japonicus genome, among which annotation was available for 23,986 genes relying on information regarding known proteins in public databases. M. japonicus is commercially valuable because of its coloration and capability for live transport. A gene involved in heme oxygenase (decyclizing) activity and heme oxidation was identified under positive selection in M. japonicas. The truncated protein had an altered helical structure, which might be responsible for resistance to low oxygen, and even the colorful shell of M. japonicus. The high-quality genome assembly enabled the identification of genes associated with cold-stress and cold tolerance in kuruma shrimp through the comparison of eyestalk transcriptomes between the low temperature stressed shrimp and normal temperature shrimp. The genome assembly presented here could be useful in future studies to determine the genetic changes underpinning the ecological traits of M. japonicus, and provide insights for genome assisted breeding.