Phosphonates in the ocean are a kind of potential phosphorus (P) source which could be utilized by phytoplankton. Although dinoflagellates cannot directly utilize phosphonates themselves, their symbiotic bacteria have the capability to degrade phosphonates into phosphate, thereby promoting the growth of algal cells. However, no studies focusing on a specific bacteria strain have been conducted thus far. In this study, Prorocentrum donghaiense was cultured under conditions with 2-Aminoethylphosphonic acid (2-AEP) as the sole P source. Isolation and purification of the symbiotic bacteria from the culture was conducted and five kinds of bacteria were obtained. Genome sequencing results revealed the presence of two types of C-P lyase pathways in the bacterial strain designated as Yoonia sp. PD-AEP-1. The function of the bacteira strain was verified through the co-culture of bacteria and algal cells. The results demonstrated that after the algal cells were treated to phosphorus-starved condition, when 2-AEP and the bacteria suspension were added together, as compared to conditions which only 2-AEP or the bacterial suspension of PD-AEP-1 was introduced, both the growth rate of algal cells and the phosphate concentration in the cultures showed a significant increase. Meanwhile, alkaline phosphatase activity and non-photochemical quenching of the algal cells decreased significantly, indicating that PD-AEP-1 has the ability to degrade 2-AEP into phosphate, thereby alleviating phosphorus limitation for P. donghaiense cells and effectively promoting the growth of algal cells. The study suggests that symbiotic bacteria of P. donghaiense might play a part in providing P sources to the algal cells through the degradation of phosphonates. This process could probably contribute to the outbreak of P. donghaiense bloom, highlighting the importance of algae-bacteira interactions in marine ecosystems.