The ichthyotoxic and mixotrophic prymnesiophyte Prymnesium parvum is known to produce dense virtually monospecific blooms in marine coastal, brackish, and inshore waters. Fish-killing Pyrmnesium blooms are often associated with macronutrient imbalanced conditions based upon shifts in ambient nitrogen (N):phosphorus (P) ratios. We therefore investigated nutrient-dependent cellular acclimation mechanisms of this microalga based upon construction of a normalized expressed sequence tag (EST) library. We then profiled the transcriptome of P. parvum under nutrient-replete conditions as well as under nitrogen (N) and phosphorus (P) limitation via microarray analyses. Twenty-three genes putatively involved in acclimation to low nutrient levels were identified, among them three phosphate transporters, which were highly upregulated under P-starvation. In contrast, the expression of genes involved in transport and acquisition of ammonium or nitrate/nitrite was unaltered in N-starved cells. We propose that genes upregulated under P- or N-starvation lend themselves as potential tools to monitor nutrient limitation effects at the cellular level and indirectly the potential for initiation and maintenance of toxic blooms of P. parvum. © 2012 Elsevier B.V.