The Baldchin Groper (Choerodon rubescens) is a Western Australian endemic species, found along the inshore reefs of the central and southern coast, particularly around the Houtman Abrolhos Islands. It inhabits rocky and coral reef habitats, often in areas with strong currents. This assembly was produced by Ocean Genomes. It 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/Computational-Biology-OceanOmics) 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.