Monotaxis heterodon (Bleeker, 1854) is widespread in the Indo-Pacific Ocean, however, it was reported that Monotaxis grandoculis (Forsskål, 1775) was the single species of Monotaxis in this area. We collected four M. heterodon specimens from the lagoon waters of Mischief Reef in South China Sea. A morphometric study was taken to confirm the occurrence of M. heterodon in the seawaters of the South China Sea and thoroughly separate them from M. grandoculis. In addition, DNA barcoding was taken for the classification of specimens. The mean genetic distance within M. heterodon group was 0.24 percentage points, group mean distance between M. heterodon and M. grandoculis was 8.71 percentage points. The phylogenetic analysis confirmed the existence of M. heterodon in the lagoon waters of the South China Sea. This study will contribute to species identification within this genus distributed in the South China Sea.