Harmful　algal　blooms　formed　by　certain　dinoflagellate　species　often　occur　when　environmental　nitrogen　nutrients　(N)　are　limited.　However,　the　molecular　mechanism　by　which　dinoflagellates　adapt　to　low　N　environments　is　poorly　understood.　In　this　study,　we　characterized　the　transcriptomic　responses　of　Prorocentrum　shikokuense　to　N　deficiency,　along　with　its　physiological　impact.　Under　N　deficiency,　P.　shikokuense　cultures　exhibited　growth　inhibition,　a　reduction　in　cell　size,　and　decreases　in　cellular　chlorophyll　a　and　nitrogen　contents　but　an　increase　in　carbon　content.　Accordingly,　gene　expression　profiles　indicated　that　carbon　fixation　and　catabolism　and　fatty　acid　metabolism　were　enhanced.　Transporter　genes　of　nitrate/nitrite,　ammonium,　urea,　and　amino　acids　were　significantly　upregulated,　indicating　that　P.　shikokuense　cells　invest　to　enhance　the　uptake　of　available　dissolved　N.　Notably,　upregulated　genes　included　those　involved　in　endocytosis　and　phagosomes,　evidence　that　P.　shikokuense　is　a　mixotrophic　organism　that　activates　phagotrophy　to　overcome　N　deficiency.　Additionally,　vacuolar　amino　acid　transporters,　the　urea　cycle,　and　urea　hydrolysis　genes　were　upregulated,　indicating　N　recycling　within　the　cells　under　N　deficiency.　Our　study　indicates　that　P.　shikokuense　copes　with　N　deficiency　by　economizing　nitrogen　use　and　adopting　multiple　strategies　to　maximize　N　acquisition　and　reuse　while　maintaining　carbon　fixation.　The　remarkable　low　N　adaptability　may　confer　competitive　advantages　to　P.　shikokuense　for　forming　harmful　blooms　in　DIN-limited　environments.　©　2020　Elsevier　B.V.