Delimiting species is crucial, especially for threatened and understudied organisms, because unresolved taxonomy can result in unrecognized species diversity and misallocated conservation efforts. In this study, we used an integrative taxonomic approach, incorporating genetic, morphological, and acoustic analyses, to clarify the phylogenetic relationship of the endangered Short-legged Horned Toad (Boulenophrys brachykolos) from South China. We focused on individuals from three geographically separated regions in Hong Kong, one on the mainland (Kowloon) and two on islands (Lantau Island and Hong Kong Island). Our genetic data identified Lantau Island individuals to be an evolutionarily distinct lineage, with a minimum genetic difference of 2.1% from other populations. Acoustic analysis revealed that male B. brachykolos from Lantau Island produce calls with similar frequency, but significantly higher pulse and note rate. However, morphological comparisons did not reveal significant differences among the three regions. To conclude, the B. brachykolos population from Lantau Island may represent a case of speciation in progress, and in the interim, should be treated as a distinct conservation unit.