A nine-month survey of potentially harmful microalgae was carried out in the coastal waters around Unguja Island, Zanzibar, from September 1998 to June 1999. Using a light microscope, more than 20 species were identified. These were distributed among three major microalgal groups: the cyanobacteria, mostly dominated by Trichodesmium spp; the dinoflagellates, dominated by Prorocentrum spp. and Gambierdiscus toxicus; and the diatoms, mostly Pseudo-nitzschia spp. This and other preliminary studies indicate the presence of harmful microalgae in Zanzibar waters. Further studies to assess both spatial and temporal distribution, as well as potential ecologic and economic effects, are recommended.