We analysed the sequences of three mitochondrial DNA (COⅠ), 16S rDNA, cytochrome oxidase b) and nuclear gene Tmo-4c4 to identify the phylogenetic relationship among the grouper hybrids and their parents (Epinephelus moara ♀ and Epinephelus akaara ♂; Epinephelus moara ♂ and Epinephelus akaara ♀). Among the four sequence fragments there was insertion deletion 16S rDNA but no insertion deletion in other three gene fragments which all belong to coding gene. As shown in results, in 12 sequences there were 4 haplotypes and 41 nucleotide polymorphic loci in COⅠ gene fragments (387 bp), 2 haplotypes and 21 nucleotide polymorphic loci in 16S rDNA gene fragments (529 bp), 2 haplotypes and 49 nucleotide polymorphic loci in Cyt b gene fragments (383 bp), and 6 haplotypes and 8 nucleotide polymorphic loci in 16S rDNA gene fragments (467 bp). Sequence divergences and genetic distance analysis showed that three mitochondrial gene sequences in the two crossing hybridized generations all showed 100% similarities respectively with the fragments of the female parents, but there were only 90% and 89.4% similarity in COⅠ, 96% and 96% similarity in 16S rDNA and 87% and 87.2% similarity in Cyt b with their male parents. In nuclear gene Tmo-4c4 there were 98.9% to 99.6% similarity with their female parents and 98.7% to 99.4% similarity with their male parents. The results indicated that there was no remarkable genetic difference. All above results imply that the two crossing grouper hybrids inherited from their female parents in three mitochondrial genes and there is no remarkable genetic difference in nuclear gene Tmo-4c4.