To construct the chromosome scale genome of Takifugu niphobles, we have generated 141X long reads on PacBio Sequel platform and 57X Illumina paired-end short reads on HiSeq 2500 platform from a YY male, and 70X Hi-C data from XY male. Initial genome was constructed in a hybrid method using DBG2OLC and SparseAssembler, and Minimap2 and Miniasm. Then Hi-C data was used to scaffold the genome. Pilon and arrow were used to polish the genome.