The　dinoflagellate　Karenia　mikimotoi　is　one　of　the　most　noxious　species　that　can　form　harmful　algal　blooms　in　coastal　areas　worldwide,　causing　serious　damage　to　aquaculture　and　fisheries.　In　the　present　study,　twelve　commonly　reported　candidate　genes　(cob,　cyc,　eif4e,　ef2,　mdh,　sam,　α-tub,　β-tub,　actin,　cal,　18s,　and　gapdh)　were　selected　to　evaluate　their　expression　stability　under　different　temperatures,　salinities,　phosphorus　and　nitrogen　limitation,　and　different　time　points　over　a　diel　cycle　in　K.　mikimotoi.　In　addition,　three　algorithms　(geNorm,　NormFinder,　and　BestKeeper)　were　used　to　evaluate　and　select　the　most　suitable　reference　genes.　It　was　observed　that　α-tub　and　eif4e　were　the　most　suitable　reference　genes　for　all　samples.　In　contrast,　ef2　and　18s　genes　showed　least　stability.　Further,　a　list　of　stable　genes,　including　α-tub,　eif4e,　gapdh,　and　mdh　was　generated　that　can　be　used　as　reference　genes　in　specific　environmental　condition　in　K.　mikimotoi.　The　gene　expression　profile　of　KFcp　gene　was　evaluated　over　a　diel　cycle　using　the　most　stable　reference　genes.　Results　revealed　that　the　expression　of　KFcp　with　transcripts　abundances　was　higher　in　light　period　and　lower　in　dark　period,　indicating　similar　gene　expression　profile　of　this　gene　in　typically　reported　algae.　This　study　provides　suitable　reference　genes　for　further　research　on　the　expression　and　regulation　of　genes　related　to　important　biochemical　processes　in　K.　mikimotoi,　improving　our　understanding　of　the　molecular　mechanism　of　its　behind　toxin　secretion　and　bloom　formation.　©　2019,　Springer　Nature　B.V.