The red spotted grouper Epinephelus akaara (E. akaara) is one of the most economically important marine fish in China, Japan and Southeast Asia, and is a threatened species. Despite its importance, molecular resources for E. akaara remain limited and no reference genome has been published to date. In this study, we constructed a reference quality genome of E. akara by taking advantage of long-read single molecule sequencing and de novo assembly of Oxford Nanopore Technology (ONT).