Phytoplankton plays a vital role as a significant component of the food chain and primary production in the marine environment. However, the blooming of certain phytoplankton can have a detrimental impact on aquatic ecosystems. Toxins produced by these algae can be harmful to humans and animals. This study aims to map the spatial and temporal distribution of harmful phytoplankton in the sea waters of Indonesia. The study uses literature published from 2005 to 2021 about harmful algae blooms in Indonesia. This literature is then analyzed by reviewing existing literature from reputable repositories, with the keyword harmful algae blooms in Indonesia, and visualized using R. The study results show two phyla of phytoplankton most commonly found in the waters of the Indonesian Sea, namely Ochrophyta and Myzozoa. Seventeen genera were identified as potentially harmful phytoplankton (Chaetoceros, Coscinodiscus, Pyrodinium, Nitzschia, Skeletonema, Thalassiosira, Trichodesmium, Alexandrium, Rhizosolenia, Pseudo-Nietzsche, Ceratium, Dinophysis, Noctiluca, Protoperidinium, Prorocentrum, Anabaena, and Oscillatoria), with ten of them known to be potentially toxic (Nitzschia, Cochlodinium, Trichodesmium, Alexandrium, Dinophysis, Pyrodinium, Protoperidinium, Prorocentrum, Oscillatoria, and Anabaena). The most affected areas by harmful algae blooms (HABs) in Indonesia are in western Indonesia, especially the southern part of Sumatra, Lampung, and DKI Jakarta. The analysis of the causes of HABs shows that excess nutrients, as well as domestic and anthropogenic wastes, are the leading causes of the HABs phenomenon in Indonesia.