The population genetic structure of the mantis shrimp, Oratosquilla oratoria, in Hong Kong waters was determined using 923 base pairs of mitochondrial DNA control region sequences. Samples were collected from six localities including the open-waters and sheltered bays in both the eastern and western waters of Hong Kong. Twenty-seven haplotypes were detected in 99 individuals. A high overall haplotype diversity (h = 0.886), with a low nucleotide diversity (π = 0.0026), was observed, and the haplotype minimum spanning network suggested that rapid expansion might have occurred among the total stomatopod population. Genetic homogeneity was observed over a meso-scale distance (80–100 km) whilst there were significant genetic differentiations between all pairs of the six samples. Partition of genetic variability based on hydrographic conditions did not reveal significant differentiations between: (1) eastern and western waters; and (2) open-waters and sheltered bays; but showed high levels of variation both within groups and within samples. Unexpectedly, genetic distance did not correlate with hydrographic distance among the samples. Results demonstrated a genetic patchiness pattern of O. oratoria in Hong Kong waters that may be attributable to the interplay between hydrographic conditions (e.g. salinity) and the species' life history traits.