The　availability　of　ambient　N　nutrient　is　often　correlated　with　the　occurrences　of　harmful　algal　bloom　formed　by　certain　dinoflagellates,　making　it　important　to　understand　how　these　species　might　be　responding　to　such　conditions.　Here,　transcriptome　sequencing　of　Karenia　mikimotoi　was　conducted　to　understand　the　underlying　molecular　mechanisms　by　which　this　dinoflagellate　copes　with　nitrogen　(N)　deficiency.　Transcriptomic　analysis　revealed　8802　unigenes　(3.56%)　that　were　differentially　expressed　with　＞=　2-fold　change.　Under　N-depleted　conditions,　genes　involved　in　glycolysis,　fatty　acid　metabolism,　and　the　tricarboxylic　acid　(TCA)　cycle　as　well　as　lipid　accumulation　were　significantly　upregulated.　The　elevated　expression　of　enzymes　used　in　protein　degradation　and　turnover　suggests　possible　metabolic　reconfiguration　towards　accelerated　N　recycling.　Moreover,　a　significant　increase　in　urea　transporter　was　observed,　indicating　increased　assimilation　of　organic　nitrogen　resources　as　an　alternative　in　N-depleted　cultures　of　K.　mikimotoi.　The　down-regulated　glutamate　synthase　genes　were　also　identified　under　N　deficiency,　suggesting　suppression　of　primary　amino　acid　synthesis　to　save　N　resource.　Taken　together,　results　of　this　study　show　enhanced　multiple　N　resource　acquisition　and　reuse　of　multiple　N　resources　constitute　a　comprehensive　strategy　to　cope　with　N　deficiency　in　a　dinoflagellate.