Genetic variation in the mitochondrial genome of the giant grouper Epinephelus lanceolatus(Bloch, 1790) and its application for the identification of broodstock

•The objective of this research was to establish a method for the validation of commercially F1 hybrid groupers developed for commercial aquaculture.•The complete mitochondrial genome (mtDNA) of the E. lanceolatuswas sequenced.•The sequenced genomic fragments were assembled, annotated and deposited at the NCBI GenBank.•Locus specific primers were developed and applied to test the F1 hybrids and related species of groupers in order to test for cross-amplification patterns.•The amplification profiles confirmed the maternal inheritance of mtDNA in the grouper F1 hybrid.•This method can be applied to validate hybridization events in the case of inter-specific grouper hybrids.•Analysis of the mtDNA sequence revealed a distinct variation in the D-loop (control) region.