Despite the importance of many species of Faviidae as structural-forming corals, only five species in three genera had a sequenced mitochondrial genome. We report the sixth complete mitochondrial genome in this family from the brain coral Platygyra carnosus, which is 16,463 bp in length and AT rich (67.0%). It has the typical coral mitochondrial gene arrangement, consisting of 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes and 2 transfer RNA (tRNA) genes (tRNA-Met and tRNA-Trp). The ND5 gene is interrupted by a large group I intron which contains 10 protein-coding genes and 12S rRNA. Compared with related species from the same family, the three non-coding regions that are longer than 200 bp are less conserved in sequences than the coding regions, indicating potential markers for population genetic studies.