The Stomatopoda (Crustacea: Malacostraca) from the South China Sea region are of commercial importance and although limited studies have been conducted on the adults, no research has ever been attempted on the larval stages because of the lack of identification keys or taxonomic descriptions. In the first study of its kind in the region, DNA barcoding was used successfully to identify unknown stomatopod larvae from plankton samples. Sequences of two mitochondrial genes, namely the cytochrome c oxidase subunit-I (COI) and the large ribosomal subunit (16S) rRNA, were applied as the barcodes to match DNA sequences from unknown larval morphotypes against those of known, locally occurring adult species. Intraspecific variations for the COI and 16S rRNA genes were found to be <2.4% and <2.1% respectively in terms of Kimura 2-Parameter (K2P) divergence of the adults, whereas variations between genera ranged from 13% to 24% and 3% to 11% respectively. These results imply that both genes are suitable for use in species identification of stomatopods; thus 14 of the 16 larval morphotypes (87.5%) obtained in Hong Kong waters can be identified to seven species through DNA barcoding. The findings of this study would also facilitate future research on the larval ecology and phylogenetic relationship of these crustaceans.