The toxic prymnesiophyte Prymnesium parvum has been linked to massive fish kills worldwide. The toxic blooms have been shown to be derived from a seed population, abiotic conditions such as temperature, salinity and water turbulence having encouraged massive growth of the Prymnesium population. Within its highly fluctuating coastal marine niche, P. parvum must acclimate rapidly to changing conditions. Although studies on the physiology and toxicity of P. parvum exist, examination of gene expression in such analyses is novel. In this study we investigate (1) relative toxicity (intracellular vs. extracellular) and (2) differential gene expression of three polyketide synthase (PKS) transcripts via real-time PCR (qPCR). It was hypothesized that these genes play a role in the production of the toxic compounds prymnesin-1 and -2 produced by P. parvum. We found that low salinity shock and high irradiation shock increase different aspects of Prymnesium's toxicity (intra- vs. extracellular). Furthermore, we found that these two physiological shock treatments induced higher copy numbers in selected polyketide synthase genes (PKS) genes, suggesting a connection between toxicity and the PKS biosynthetic pathway. Our results demonstrate that PKS genes are likely to play an important role in the toxicity of P. parvum and deserve further investigation in populations exposed to changing environmental conditions. © 2011 British Phycological Society.