In this study, we reported the complete mitochondrial DNA sequence of the hybrid grouperEpinephelus fuscoguttatus(♀)×Epinephelus lanceolatus(♂). The full-length of the mitochondrial genome consisted of a 16,644 bp fragment, with the base composition of A (29.21%), C (26.84%), G (15.65%) and T (28.29%). It contained 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and a major non-coding control region (D-loop region). The composition and order of these genes were identical to most other vertebrates. All the protein initiation codons were ATG, except that COX1 began with GTG and ATP-6 was not determined. The complete mitogenome of the hybridE. fuscoguttatus(♀)×E. lanceolatus(♂) provided an important data set for the study in genetic mechanism of the hybridization. [ABSTRACT FROM PUBLISHER]