Clownfish and their associated sea anemones are icons of tropical and subtropical coastal ecosystems, but bleaching and collecting for the aquarium trade has reduced their population densities in several Indo-Pacific locations. We surveyed four Entacmaea quadricolor populations and their associated clownfish Amphiprion clarkii in Hong Kong. These assemblages represented a combination of exposed and sheltered, flat bottomed and sloped conditions. Different from tropical areas, where E. quadricolor is usually found in sheltered shallow waters, the four populations in Hong Kong were distributed in 4–10 m depths, being densest on a 40 × 80 m slope of volcanic rocks (34.2–76.6% substrate cover and 48.7–102.1 ind  m−2) at an exposed site. This distribution pattern could be explained by the high turbidities associated with river discharge and sedimentation rates in local waters, which discourage the establishment of E. quadricolor populations in sheltered bays; shallow habitats might not be suitable for E. quadricolor in Hong Kong due to strong wave actions generated by typhoons. Amphiprion clarkii was present at low densities (0.07–0.26 fish m−2) across the sites. Our data provide a baseline for monitoring the changes of these conspicuous members of shallow water communities in Hong Kong.