We have constructed a genomic bacterial artificial chromosome (BAC) library from homozygous cloned Japanese flounder Paralichthys olivaceus using the pBAC-lac vector. This BAC library consists of about 49,100 clones and is deposited in 128 microtiter plates with 384 wens. The average size of inserted DNA was calculated to be 165 kb. The BAC library was determined to cover 9 times the Japanese founder haploid genome. The Japanese flounder genomic EPIC library will be useful for gene isolation as well as quantitative trait loci (QTL) analysis.