Montipora vietnamensis Veron, 2000 (Cnidaria, Anthozoa, Scleractinia, Acroporidae) is an uncommon, but distinctive species of stony coral. The complete mitochondrial genome of M. vietnamensis was sequenced in this study for the first time, based on 32 pairs of primers newly designed according to seven species in the family Acroporidae. The mitogenome of M. vietnamensis has a circular form and is 17,885 bp long, including 13 protein-coding genes (PCGs), 2 tRNA (tRNA^Met, tRNA^Trp), 2 rRNA genes and a putative control-region. The base composition of the complete mitogenome was 24.8% A, 14.2% C, 24.2% G and 36.8% T, with a higher AT content (61.6%) than GC content (38.4%). Based on 13 protein-coding genes, a Maximum Likelihood phylogenetic analysis showed that M. vietnamensis is clustered in the genus Montipora which belongs to the family Acroporidae. More stony coral species should be sequenced for basic molecular information and to help confirm the taxonomic status and evolutionary relationships of Scleractinia in the future.