Long-SAGE (serial analysis of gene expression) was used to profile the transcriptome of the brown tide-forming alga, Aureococcus anophagefferens, under nutrient replete (control), and nitrogen (N) and phosphorus (P) deficiency to understand how this organism responds at the transcriptional level to varying nutrient conditions. This approach has aided A. anophagefferens genome annotation efforts and identified a suite of genes upregulated by N and P deficiency, some of which have known roles in nutrient metabolism. Genes upregulated under N deficiency include an ammonium transporter, an acetamidase/formamidase and two peptidases. This suggests an ability to utilize reduced N compounds and dissolved organic nitrogen, supporting the hypothesized importance of these N sources in A. anophagefferens bloom formation. There are also a broad suite of P-regulated genes, including an alkaline phosphatase, and two 5′-nucleotidases, suggesting A. anophagefferens may use dissolved organic phosphorus under low phosphate conditions. These N- and P-regulated genes may be important targets for exploring nutrient controls on bloom formation in field populations.