Urbanization and associated human activities have caused numerous changes to natural environments, including the loss of natural habitats and replacement with artificial structures. How these changes impact coastal marine biodiversity and ecosystem functioning is not well known. In this study, we examined the potential impacts of habitat changes by comparing species commonality and community structure (i.e., species richness, abundance, and functional composition) among artificial (a breakwater wall) and natural habitats (eelgrass bed, intertidal flat, and subtidal bottom) within a semi-enclosed coastal sea impacted by marine urbanization. We found considerable species overlap (i.e., high species sharing) among the eelgrass bed, intertidal flat, and subtidal bottom habitats. By contrast, the breakwater wall was a distinctive habitat with little overlap in species and functional groups with the other habitats, and was therefore a poor substitute for natural habitats. Our study suggests that marine urbanization degrades redundancy and inhibits the maintenance of biodiversity in coastal marine zones.