Population genetics is a tool that conservationists have continued to rely on to quantify population-level genetic variation and identify priority conservation units. The range-wide deforestation starting in the 1600s and rapid urban development and associated habitat modification in recent decades have posed significant challenges to the Hong Kong newt (Paramesotriton hongkongensis), a tropical salamander restricted to streams and forests in southern China. Our research, which sampled 310 adult P. hongkongensis from 10 breeding streams throughout its current distribution in Hong Kong, China to quantify genetic diversity and characterize its population genetic structure using 9 pairs of SSR primers, has revealed crucial insights. Despite long-term, repeated disturbance to its habitat and fragmentation caused by urban development, genetic diversity has been maintained within and among P. hongkongensis populations. Only two out of ten sites exhibited evidence of population bottlenecks. Bayesian clustering revealed five well-supported clusters within the range of P. hongkongensis in Hong Kong, which should be managed as separate conservation units. This work adds to the existing evidence that the effects of urbanization and human disturbance on genetic diversity in amphibians are not easily generalizable and should be addressed on a case-by-case basis.