The haptophyte Prymnesium parvum is known to cause massive fish kills during its blooms. The toxicity of P. parvum is attributed to its ability to produce prymnesins, a group of supersized ladder-frame polyether compounds. This group of toxins can be further divided into three different types (A-, B- and C- type), which present further diversity in terms of number and chemical structure of derivatives. In the present study, we used nine P. parvum strains representing all three types of prymnesins to elucidate the molecular mechanisms involved in prymnesin biosynthesis. Due to the polyketide nature of prymnesins, particular attention was paid to polyketide synthase genes (PKSs). The transcriptomes of all nine P. parvum strains were screened for the presence of PKS genes. A mean of 25 contigs containing multi-modular type I PKS ketosythase (KS) domains were found per strain, which were subsequently used to assess the evolutionary history of prymnesin production. The phylogenetic analysis of the KS domains showed that, compared to KS transcripts from other organisms, they form distinct clades as well as clades corresponding to each prymnesin type. In addition, a comparative transcriptomic analysis of all strains revealed the presence of candidate genes involved in the biosynthesis of specific prymnesin derivatives. The current study will contribute to a better understanding of the mechanisms of toxin production in P. parvum in order to develop efficient tools for monitoring purposes.