we preformed a genomic survey for C. japonicus using next generation sequencing technology at the first, investigated its genomic feature and reconstructed the phylogenomic relationship with single copy orthologs genes of C. japonicus. The draft genome assembly of C. japonicus can help us find more useful information for the taxonomic, adaptive evolutionary mechanisms, phylogenetic studies and understand the genome evolution of genus Chirolophis, as well as provide a molecular basis of C. japonicus.