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The ability to utilize organic phosphorus is believed to confer competitive advantages to dinoflagellates and some other phytoplankton species that form harmful algal blooms. However, the mechanisms regulating the utilization of the diverse organophosphate compounds are still poorly understood. In this study, we investigated the utilization of adenosine triphosphate (ATP) and the molecular mechanism in Karenia mikimotoi, a cosmopolitan HAB forming dinoflagellate. Cultures were set up in L1 medium as control (+P group), dissolved inorganic phosphorus (DIP)-depleted L1 medium (-P group), and ATP-amended –P medium (ATP group). Differential gene expression was profiled for ATP and +P groups using suppression subtractive hybridization (SSH), 454 pyrosequencing, and RT-qPCR methods. Results showed that ATP supported a similar growth rate and cell yield as L1 medium. We observed DIP release from ATP into the medium in the course of the experiment, suggesting that K. mikimotoi cells were expressing extracellular DOP hydrolases. Additionally, we confirmed that both the phosphorus and nucleoside components of ATP could be assimilated by K.mikimotoi for further utilization. Gene expression analyses revealed that genes involved in the metabolic pathway of ATP such as phosphate transporter, Canalicular multispecific organic anion transporter 1, and some genes related to purine metabolism were up-regulated in the ATP cultures. Meanwhile, we also identified genes related to key functional categories of energy, metabolism, and protein synthesis. Our results reveal the general rhythmicity of ATP assimilation, and provide insights into possible target genes and proteins for further research of phosphorus utilization mechanisms in K. mikimotoi and other dinoflagellates.