Variation in life history characteristics is believed to play an important role in dispersal and thus shaping the population and genetic structure of marine invertebrates. The genetic structure of Ibla cumingi, a small intertidal stalked barnacle that broods lecithotrophic larvae, was evaluated using 145 random amplified polymorphic DNA markers on 100 individuals from five locations across Hong Kong waters. Shallow genetic structure was observed along open-coast shores, and there was no indication of isolation by geographical distance. A significant genetic divergence, however, was observed between samples inside and outside Tolo Harbour, a semi-enclosed, sheltered and estuarine bay located in the north-eastern quadrant of Hong Kong, indicating the presence of a genetic sub-structuring pattern. In addition, relatively lower genetic diversities were described for samples inside Tolo Harbour than those from open-coast shores. This could be associated with an increase in inbreeding events attributed to local settlement caused by larval retention. This study provides an insight into how the interaction of life history and local, enclosed, hydrographic conditions could result in a substantial genetic structuring of I. cumingi over a meso-scale geographical distance.