Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophis japonicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C. japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C. japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C. japonicus is closely related with Anarrhichthys ocellatus, Cebidichthys violaceus, and Pholis gunnellus. The results provide more thorough genetic information of C. japonicus and a theoretical basis and reference for further genome-wide analysis.