Caridina cantonensis Yu 1938 is an atyid shrimp that is widespread in southern China, including Hong Kong. It is a fully freshwater species with an abbreviated larval development lacking planktonic stages. The population genetics of C. cantonensis in Hong Kong streams was studied at inter- and intradrainage scales using random amplified polymorphic DNA (RAPD) markers. Shrimps displayed low levels of within-population genetic variation (≤20% of total genotypic variance) but high levels of among-population variation (>50% of total genotypic variance) at both scales. High interdrainage genetic differentiation indicated that dispersal among catchments was limited, whereas high differentiation among populations at the intradrainage scale mainly resulted from natural barriers such as waterfalls. The effect of man-made barriers on population differentiation at the intradrainage scale was less marked than at the interdraineage scale. Levels of gene flow among populations within and among drainage systems were low, the estimated number of effective migrants/generation (N_em) was <0.1, and there was a trend toward relatively fewer alleles and lower heterozygosity in upstream populations than in downstream populations. Genetic differentiation between lowland populations from adjacent drainages was lower than for other pairwise combinations of populations, suggesting that interdrainage dispersal is likely during floods. The genetic structure of C. cantonensis populations in Hong Kong streams indicates that adaptation to local conditions in individual streams or sites within streams probably occurred. At a regional scale, this process might account for the large number of stenotopic species of Caridina in Asia.