Globally, there are 3 400 to 4 000 described species of marine microalgae but only 1 to 2 percent are considered to be harmful. Harmful algal blooms (HABs) have significant impacts on food safety and security through contamination or mass mortalities of aquatic organisms. The impacts and mass mortalities of marine species caused by harmful algae are not new and have been recorded for decades. However, there is growing concern that these events will increase due to accelerating global warming, climate change and anthropogenic activities. Indeed, if not properly controlled, aquatic products contaminated with HAB biotoxins are responsible for potentially deadly foodborne diseases and when rapidly growing, HAB consequences include reduced dissolved oxygen in the ocean, dead zones, and mass mortalities of aquatic organisms. Improving HAB forecasting is an opportunity to develop early warning systems for HAB events such as food contamination, mass mortalities, or foodborne diseases. Surveillance systems have been developed to monitor HABs in many countries; however, the lead-time or the type of data (i.e. identification at the species-level, determination of toxicity) may not be sufficient to take effective action for food safety management measures or other reasons, such as transfer of aquaculture products to other areas. Having early warning systems could help mitigate the impact of HABs and reduce the occurrence of HAB events. The Joint FAO-IOC-IAEA technical guidance for the implementation of early warning systems (EWS) for HABs will guide competent authorities and relevant institutions involved in consumer protection or environmental monitoring to implement early warning systems for HABs present in their areas (marine and brackish waters), specifically those affecting food safety or food security (benthic HABs, fish-killing HABs, pelagic toxic HABs, and cyanobacteria HABs). The guidance provides a roadmap for stakeholders on how to improve or implement an EWS for HABs and biotoxins, where appropriate. It is important to note that not all countries and institutions can implement the same level of EWS for HABs, and this guidance is intended mainly for those who seek to broaden existing early warning systems, or who are just beginning to consider putting a system in place.