The Brilliant Pomfret (Eumegistus illustris) is found in the Indo-Pacific region, including the western equatorial Indian Ocean and the Pacific Ocean from Okinawa (Ryukyu Islands) to Fiji, Tuvalu, and Hawaii. This species inhabits marine benthopelagic zones at depths ranging from 1 to 620 meters. This assembly is based on PacBio HiFi long reads, Dovetail Omni-C libraries and Illumina short reads. Data was generated at the Minderoo OceanOmics Centre at the University of Western Australia and assembled in house using a custom pipeline (https://github.com/MinderooFoundation) that follows Vertebrate Genomes Project workflows (https://vertebrategenomesproject.org/). The raw data and version 1 assembly are made available and should be credited in accordance with Ocean Genomes data use and sharing policies URL: https://www.minderoo.org/oceanomics. To discuss interim access, please contact oceangenomes@uwa.edu.au.