Large bryozoan colonies can form bryozoan biogenic habitats, which significantly enhance habitat complexity and associated biodiversity. Globally, these habitats are rare and threatened by anthropogenic activities. Our study presents newly discovered bryozoan biogenic habitats in Western Port, Australia (~70 km SE of Melbourne) and further expands our current knowledge of bryozoan habitats in other parts of the bay. Imagery obtained during ROV and scuba diving surveys revealed undescribed bryozoan biogenic habitats comprised of non-fenestrate bryozoans that develop erect plates, growing large colonies (up to 1m in circumference and vertical relief) in high-energy areas in the North and Western Arms of Western Port. These bryozoan habitats represent ‘hotspots’ of biodiversity compared to the surrounding sediment habitats, with sponges, ascidians, molluscs, echinoderms, fishes, cnidarians, smaller, soft branching bryozoan species and macroalgae recorded. The North and Western Arm bryozoan habitats differ profoundly from the previously-described, shallower bryozoan habitats in the Eastern Arm dominated mostly by fenestrate species forming mounds and located in shallower, low-energy areas. The new findings add to an emerging understanding of bryozoan biogenic habitats in Western Port (a RAMSAR site of international significance), which are unique in their ecophysical setting and one of only four known such habitats in Australia.