| Summary: | Groupers are commercial, mainly reef-associated fishes, classified in the family Epinephelidae (Perciformes). This study first sequenced the complete mitogenomes of <i>Cephalopholis leopardus</i>, <i>Cephalopholis spiloparaea</i>, <i>Epinephelus amblycephalus</i>, and <i>Epinephelus hexagonatus</i>. The lengths of the four Epinephelidae mitogenomes ranged from 16,585 base pair (bp) to 16,872 bp with the typical gene order. All tRNA genes had a typical cloverleaf structure, except the tRNA-<i>Ser</i> (AGY) gene which was lacking the entire dihydrouridine arm. The ratio of nonsynonymous substitution (Ka) and synonymous substitution (Ks) indicated that four groupers were suffering a purifying selection. Phylogenetic relationships were reconstructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on all mitogenomic data of 41 groupers and 2 outgroups. The identical topologies result with high support values showed that <i>Cephalopholis</i> and <i>Epinephelus</i> are not monophyletic genera. <i>Anyperodon</i> and <i>Cromileptes</i> clustered to <i>Epinephelus</i>. <i>Aethaloperca rogaa</i> and <i>Cephalopholis argus</i> assembled a clad. <i>Cephalopholis leopardus</i>, <i>C. spiloparaea</i>, and <i>Cephalopholis miniata</i> are also in a clade. <i>Epinephelus</i><i>hexagonatus</i> is close to <i>Epinephelus tauvina</i> and <i>Epinephelus merra</i>, and <i>E. amblycephalus</i> is a sister group with <i>Epinephelus stictus</i>. More mitogenomic data from Epinephelidae species are essential to understand its taxonomic status with the family Serranidae.
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