Malaysia is one of the countries in the Southeast Asia region that is badly affected by Harmful Algal Blooms (HABs). Since the first report of Pyrodinium bahamense in 1976, despite no clear increasing trend in the frequency of toxic blooms observed over the past three decades, the occurrence and blooms of other PST producers such as Alexandrium minutum, Alexandrium tamiyavanichii and Gymnodinium catenatum have become a concern. The frequent fish-killing algal blooms of Margalefidinium polykrikoides, Tripos furca, Chattonella spp., and unarmored dinoflagellates (e.g., Karlodinium australe) have resulted in severe economic damage to mariculture industries. This presentation will share the recent finding of HABs research in Malaysia. The blooms of Alexandrium minutum and underlying mechanism at the semi-enclosed lagoon over the four months blooms will be revealed. Massive fish kill events, the culprit, and the mechanism involved in these fish kill incidents were clarified. The risk of Amnesic shellfish poisoning (ASP) in the country was assessed, and the potential toxic diatom Pseudo-nitzschia and Nitszchia spp. were identified, including novel toxic species. The seasonal changes of Benthic Harmful algal communities at different microhabitats were further examined based on a three-year study at Perhentian island. The use of next-generation sequencing and metabarcoding to assess the distribution of harmful algal species in Malaysian coastal water covering a distance of more than 1000km will be discussed.   More studies are needed to understand the long-term changes of HABs for better management of mitigation of the impacts.