Phosphorus (P) deficiency has significant impacts on the growth and metabolism of macroalgae in marine environments. To cope with P deficiency, algae have evolved several adaptive strategies, including the utilization of dissolved organic phosphorus. However, little is known about the DOP utilization in Neopyropia yezoensis, particularly the molecular mechanisms involved in DOP assimilation and response to P deficiency within this species. In this study, transcriptome analysis was performed to explore the key signaling pathways associated with the response of N. yezoensis to glucose-6-phosphate utilization and P deficiency.