Phosphorus (P) is one of the major macronutrients necessary for phytoplankton growth. In some parts of the ocean, however, P is frequently scarce, hence, there is limited phytoplankton growth. To cope with P deficiency, phytoplankton evolved a variety of strategies, including, utilization of different P sources. Polyphosphate (polyP) is ubiquitously present and serves an essential function in aquatic environments, but it is unclear if and how this polymer is utilized by phytoplankton. Here, we examined the physiological and molecular responses of the widely present harmful algal bloom (HAB) species, Heterosigma akashiwo in polyP utilization, and in coping with P-deficiency. Our results revealed that two forms of inorganic polyP, namely, sodium tripolyphosphate and sodium hexametaphosphate, support H. akashiwo growth as efficiently as orthophosphate. However, few genes involved in polyP utilization have been identified. Under P-deficient conditions, genes associated with P transport, dissolved organic P utilization, sulfolipid synthesis, and energy production, were markedly elevated. In summary, our results indicate that polyP is bioavailable to H. akashiwo, and this HAB species have evolved a comprehensive strategy to cope with P deficiency.