Rhodoliths are benthic calcium carbonate nodules accreted by crustose coralline red algae which recently have been identified as useful indicators of biomineral changes resulting from global climate change and ocean acidification. This study highlights the discovery that the interior of rhodoliths are marine biodiversity hotspots that function as seedbanks and temporary reservoirs of previously unknown stages in the life history of ecologically important dinoflagellate and haptophyte microalgae. Whereas the studied rhodoliths originated from offshore deep bank pinnacles in the northwestern Gulf of Mexico, the present study opens the door to assess the universality of endolithic stages among bloom-forming microalgae spanning different phyla, some of public health concerns (Prorocentrum) in marine ecosystems worldwide.