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Harmful algal blooms (HABs) were not new to the tropical semi-enclosed Johor Strait, with incident records that could trace back to the 1980s. HAB monitoring in the area, often, is reactive, focusing only on HAB taxa previously causing problems but neglecting potential emerging HABs. To develop datasets on HABs that can better inform and improve management practices, monitoring should expand to sample whole microphytoplankton communities. In this study, microphytoplankton community structure across the Strait was investigated. Abundances o