The giant grouper, Epinephelus lanceolatus, is the largest grouper species and the largest coral reef dwelling bony fishes in the world. Despite its extremely fast growth performance and great economic importance, genetic control of growth traits in this species is poorly known. In this study, we performed a genome-wide association study of growth traits in E. lanceolatus using 42323 single nucleotide polymorphism (SNPs) obtained by genotyping-by-sequencing. We identified a total of 36 growth-related SNPs, of which eight SNPs reached genome-wide significance level. Also, we found 22 quantitative trait locus (QTL) including nine significant QTL on linkage groups (LG) 1, 4, 5, 7, 9, 10, 15, 17 and thirteen suggestive QTL on LG 1, 6, 7, 8, 9, 10, 13, 14, 15, 17, 19, 24, thereby implying that polygenic regulation of growth traits in the giant grouper. The phenotypic variance explained by these QTL varied from 7.24 for body height to 18.42 for body length. Interestingly, the QTL (LG17:6934451) was shared between body weight and body height. Two genome QTL (LG7: 22596399 and LG5: 11877836) for body length were also consistent with the associated regions of total length at chromosome-wide level. Eight potential candidate genes containing or near (within 100kb) the identified significant SNPs were selected for expression analysis, in which four genes (PITPNC1, PTPRE, ABHD17C and VEGFAA) were differentially expressed. Our results could facilitate better understanding for genetic architecture of growth in the giant grouper and laid a foundation for marker-assisted selection or genomic selection for other grouper species.