Amphidinium Claparede et Lachmann is one of the most abundant and diverse dinoflagellate genera found in marine benthic, sand dwelling and pelagic habitats. Species of Amphidinium have been widely studied for their potential to produce natural products, in particular, long chain and linear polyketide and macrolide compounds. More than 40 compounds produced by different species of Amphidinium have been isolated. These compounds with varying bioactivities are being investigated for their efficacy as antimicrobial and/or therapeutic agents. Some compounds produced by Amphidinium species have bioactivities against fish gill cells, and may lead to fish kills. Structural elucidation of many toxic compounds produced by dinoflagellates suggest that they may be based on a polyether ladder backbone, and that polyketide synthase (PKS) enzymes may have a role in their biosynthesis. The aim of our study was to screen Amphidinium species for the production of polyketide compounds and test their toxicity. We conducted a transcriptomic sequencing study to determine the presence of PKS genes (both mono-functionally expressed catalytic domains and genes encoding multimodular PKS enzyme complexes) in Amphidinium. The ketosynthase domain encoding transcripts were found to form distinct clades in the phylogenetic analysis, in comparison to similar genes from other organisms. We also show the presence of genes encoding six key enzymes essential for fatty acid production in Amphidinium. The results presented here are a step forward towards recognising the genes encoding critical steps in toxin biosynthesis and designing tools to monitor for and mitigate human illnesses due to harmful algal blooms.