Understanding population connectivity is crucial for effective conservation management. Schemes for speculating potential connectivity patterns over large to medium geographic scales using riverscape and life history features have been developed, but whether they are still applicable over fine scales has rarely been examined. Caridina shrimps (Family Atyidae) constitute a major component of freshwater ecosystems. Nonetheless, although over 20% of atyid species are considered Threatened or Near Threatened on the International Union for Conservation of Nature Red List, a general lack of understanding of the population structure of these species, which typically have restricted distributions, significantly hampers conservation management. Here, we examined the fine-scale population structure of five atyid species in Hong Kong, a highly urbanised metropolis, using the mitochondrial cytochrome oxidase subunit I (COI) gene and four to six microsatellite markers. The results reveal species-specific contrasting phylogeographic patterns, ranging from wide-range genetic panmixia to population differentiation at an extremely small scale of <1 km. This pronounced population structuring may be attributed to the freshwater obligates’ limited dispersal ability, high level of inbreeding and marked demographic fluctuations associated with climate changes since the Pleistocene. The results shed new light on the evolution of this widely distributed shrimp genus and bridge the critical knowledge gap in formulating effective conservation plans.