Background <p>The gray snapper (<i>Lutjanus griseus</i>) is a marine reef fish commonly found in coastal and shelf waters of the tropical and subtropical western Atlantic Ocean. In this work, a draft reference genome was developed to support population genomic studies of gray snapper needed to assist with conservation and fisheries management efforts.</p> Methods and results <p>Hybrid assembly of PacBio and Illumina sequencing reads yielded a 1,003,098,032 bp reference across 2039 scaffolds with N50 and L50 values of 1,691,591 bp and 163 scaffolds, respectively. A linkage map was generated by genotyping parents and 286 offspring of a single pair cross using the double digest Restriction Associated DNA (ddRAD) protocol. The map featured 10,965 informative markers that were assigned to 24 linkage groups and used to scaffold the assembly. The anchored assembly spanned 962,844,722 bp (N50 = 41,865,368 bp, L50 = 11 scaffolds) in 24 pseudo chromosomes and yielded a BUSCO score of 95.2%. Annotation of the final assembly in Augustus revealed 39,070 candidate genes. Gene ontology annotation was obtained for 48.8% of the predicted genes. Analysis of shared syntenic regions revealed that each gray snapper chromosome matched a unique Japanese medaka, <i>Oryzias latipes,</i> counterpart and the reference showed a high degree of synteny with the closely related <i>Lutjanus erythropterus</i> assembly.</p> Conclusions <p>This resource will greatly enhance genomic studies of conservation and management of natural populations as well as efforts to develop breeding programs for this species and other lutjanids.</p>