A cDNA library was constructed from late log-phase cultures of the ichthyotoxin-producing haptophyte, Prymnesium parvum. Approximately 6,300 single-pass 5' nucleotide sequences (out of nearly 8,000 randomly isolated clones) achieved length and quality criteria for incorporation into an expressed sequence tag (EST) database. Collectively, 3,415 unique genes (tentative unigenes [TUGs]) were assembled. Database searches revealed approximately 1,100 TUG (34%) that encode proteins of known or putative function (expect values E < or = 1.0 x 10(-10)), representing most functional classes of proteins and many metabolic pathways. In addition to proteins involved in photosynthesis and protein synthesis/degradation, one of the most frequently encountered transcripts putatively encodes an ABC-type phosphate transport system component. Active (and efficient?) phosphate transport may correlate with rapid growth, perhaps explaining how this alga out-competes other species when it blooms and becomes toxic under low-phosphate conditions. The majority of TUGs, including 12 of the 50 most commonly encountered transcripts, encode potentially novel proteins, some of which are probably involved in synthesis and secretion of the unique prymnesin toxins. This work suggests that future studies on the expression of many of these genes during rapid growth should provide insight into the genetic basis of bloom formation and toxicity.