Karenia mikimotoi is one of the most well-known harmful bloom species in temperate coastal waters. The present study investigated the characteristics of alkaline phosphatase (APase) and phosphodiesterase (PDEase) activities in hydrolysis of two phosphomonoesters (adenosine triphosphate (ATP) and ribulose 5-phosphate (R5P)) and a phosphodiester (cyclic adenosine monophosphate (cAMP)) in K. mikimotoi and compared its growth and physiological responses to the different forms of phosphorus substrates. K. mikimotoi produced comparable quantities of APase and PDEase to hydrolyze the organic phosphorus substrates, although hydrolysis of the phosphomonoesters was much faster than that of the phosphodiester. The growth of K. mikimotoi on organic phosphorus substrates was comparable to or better than that on inorganic phosphate. The difference in particulate organic nutrients (carbon, nitrogen, and phosphorus) and hemolytic activity supported different rates of hydrolysis-assimilation of the various organic phosphorus substrates by K. mikimotoi. The hemolytic activities of K. mikimotoi in the presence of organic phosphorus substrates were several times those in the presence of inorganic phosphate during the exponential phase. This suggested the potential important role of organic phosphorus in K. mikimotoi blooms.