Harmful　algal　blooms　(HABs)　have　increased　as　a　result　of　global　climate　and　environmental　changes,　exerting　increasing　impacts　on　the　aquatic　ecosystem,　coastal　economy,　and　human　health.　Despite　great　research　efforts,　our　understanding　on　the　drivers　of　HABs　is　still　limited　in　part　because　HAB　species＇　physiology　is　difficult　to　probe　in　situ.　Here,　we　used　molecular　ecological　analyses　to　characterize　a　dinoflagellate　bloom　at　Xiamen　Harbor,　China.　Prorocentrum　donghaiense　was　identified　as　the　culprit,　which　nutrient　bioassays　showed　were　not　nutrient-limited.　Metatranscriptome　profiling　revealed　that　P.　donghaiense　highly　expressed　genes　related　to　N-　and　P-nutrient　uptake,　phagotrophy,　energy　metabolism　(photosynthesis,　oxidative　phophorylation,　and　rhodopsin)　and　carbohydrate　metabolism　(glycolysis/gluconeogenesis,　TCA　cycle　and　pentose　phosphate)　during　the　bloom.　Many　genes　in　P.　donghaiense　were　up-regulated　at　night,　including　phagotrophy　and　environmental　communication　genes,　and　showed　active　expression　in　mitosis.　Eight　microbial　defense　genes　were　up-regulated　in　the　bloom　compared　with　previously　analyzed　laboratory　cultures.　Furthermore,　76　P.　donghaiense　microRNA　were　identified　from　the　bloom,　and　their　target　genes　exhibited　marked　differences　in　amino　acid　metabolism　between　the　bloom　and　cultures　and　the　potential　of　up-regulated　antibiotic　and　cell　communication　capabilities.　These　findings,　consistent　with　and　complementary　to　recent　reports,　reveal　major　metabolic　processes　in　P.　donghaiense　potentially　important　for　bloom　formation　and　provide　a　gene　repertoire　for　developing　bloom　markers　in　future　research.　©　2018