The role of marine protected areas is crucial in the development of sustainable fisheries and in the mitigation and adaptation to climate change and associated processes. Therefore, it is essential to monitor the types of habitats and their associated biodiversity. Macroalgae play a key role in carbon sequestration and provide habitat for numerous marine species, including larval phases of species of commercial interest. There are currently several threats that affect macroalgae highlighting overfishing, the appearance of invasive species, and changes in seawater and air temperature. ALGANAT2000 will be developed on a pilot scale in the intertidal habitat of a space of the Natura 2000 Network, the Maritime-Terrestrial National Park of the Atlantic Islands of Galicia (PNMTIAG), in order to demonstrate its usefulness as a tool for improving knowledge, management and monitoring of the abundance and ecological status of macroalgae present in marine protected areas.