Harmful events caused by benthic microalgae have recently garnered a high level of attention in temperate areas, upon reports of Ostreopsis species causing fauna damage, food intoxication and respiratory illness. A resurgence of interest has also occurred in ciguatera fish poisoning (CFP), a syndrome associated with the consumption of reef fish contaminated by ciguatoxins produced by the dinoflagellate genus Gambierdiscus in tropical and subtropical areas. To foster research on events caused by benthic microalgae, the SCOR-IOC Global Ecology and Oceanography on Harmful Algal Blooms (GEOHAB) program started a Core Research Project on Benthic Harmful Algal Blooms (BHABs). During an Open Science Meeting (OSM) in 2010, scientists studying benthic and planktonic microalgae identified the main gaps of knowledge and the research, technology and infrastructure needs in the field of the ecology and oceanography of BHABs. The issues addressed during the OSM covered the state of taxonomy, sampling methods, biogeography, genetic diversity, ecology and ecophysiology of BHABs, along with the identification of research priorities and approaches to be taken in order to improve understanding and prediction of BHABs.