The ecology of subtidal rhodolith beds has been investigated for the first time in New Zealand, characterising two rhodolith species, Lithothamnion crispatum and Sporolithon durum, examining the structure and physical characteristics of beds at two locations and documenting their associated biodiversity. Site and characteristics: Field work was conducted in the Bay of Islands, at Kahuwhera Bay and Te Miko Reef, in February and September 2010. The rhodolith beds were mapped using a combination of techniques and the physical characteristics of the habitats were assessed and compared with adjacent areas outside the rhodolith beds. The rhodolith beds differed significantly in terms of water motion, sediment characteristics and light levels, with Te Miko Reef having characteristics regarded as typical of rhodolith assemblages, and Kahuwhera Bay being atypical with respect to sediments and water clarity. The Te Miko Reef bed was in clear water and rhodoliths were clearly visible sitting on top of the substrate in a more or less single layer over rhodolith- and shell-derived gravel, whereas at Kahuwhera Bay there were fine sediments suspended in the water column and covering rhodoliths and associated biota, and live rhodoliths were in a more or less single layer overlaying grey to blackened rhodoliths in a darkly coloured rhodolith/sediment sublayer. The two rhodolith beds differed in current direction and strength with no clear tidal signal or direction of water motion at Kahuwhera Bay and tidally driven water movement at Te Miko Reef with a dominant northwest flow.