Phosphonates have been shown to be an important source of phosphorus in the nutrition of marine bacteria. Recent studies have demonstrated at least some species of eukaryotic phytoplankton are capable of utilizing phosphonates to support growth. We used RNA sequencing to investigate the transcriptional response of three species of eukaryotic phytoplankton given a phosphonate as the sole source of phosphorus. The results of this project have critically enhanced our understanding of the metabolic capabilities of phytoplankton.