Loss of habitat is considered to be one of the major threats to biodiversity. This is of concern because habitats created by bioengineering species support and enhance local biodiversity. The present study investigated the abundance and distribution of polychaetes among distinct patches of the biogenic habitats created by the tubeworm Galeolaria caespitosa, the Sydney rock oyster Saccostrea glomerata and the turfing red alga Corallina officinalis on natural rocky shores within Sydney Harbour, NSW, Australia. Assemblages of polychaetes were compared among the habitats, species of polychaetes restricted to single habitats were identified (1 species was unique to oysters or Galeolaria, and 7 species were unique to coralline turf), estimates of their contribution to diversity at the patch and landscape scale, and unique species were made. The relative cover of each of the habitats throughout Sydney Harbour is patchy but within the marine dominated sections of natural rocky shores, they are widespread. All habitats supported unique species of polychaetes and overall assemblages differed among the habitats. Loss of biogenic habitats due to climate change, harvesting or other anthropogenic activities, will result in loss of many species of polychaetes and will have larger scale implications. Future management of marine biodiversity, including the potential for a marine park network in Sydney Harbour, needs to take into account the importance of biogenic habitats in supporting these diverse assemblages of invertebrates.