Large scale disturbances associated with anthropogenic activities or natural disasters can destroy primary habitat-forming species like corals, seagrasses and seaweeds. However, little research has documented if and on how large-scale disturbances aﬀect secondary habitat formers, such as epiphytes and small animals that depend on biogenic habitats. Here we quantiﬁed changes in the abundance of both primary and secondary habitat-forming seaweeds as well as seaweed-associated invertebrates before and after a 7.8 Mw earthquake that uplifted four intertidal reef platforms by 0.5–0.8 m on the Kaikōura coastline in New Zealand. We found that the dominant primary (Hormosira banksii and three Cystophora species) and secondary (obligate and facultative epiphytes) habitat-forming seaweeds were all decimated and that mobile seaweed-associated animals were signiﬁcantly less abundant (per gram of seaweed biomass) after the earthquake. Importantly, epiphytes became functionally extinct after the earthquake, as less than 0.1 % of the populations survived, whereas primary habitat formers survived in suitable microhabitats, like water covered tide-pools and tidal channels. Based on these results we also discuss possible cascading ecosystem eﬀects and future scenarios for natural recovery vs. active restoration that could speed up the recovery of habitat-forming species on degraded reefs.