<p>Freshwater dinoflagellates are typically considered non-toxic, and their polyketides and toxin biosynthesis genes are largely unexplored. Here, we generated and analyzed the transcriptome of freshwater dinoflagellate <i>Palatinus apiculatus</i> and compared it with the transcriptome data from <i>Peridinium bipes</i> and <i>Ceratium furcoides</i> to investigate the presence and diversity of polyketide synthases (PKS), fatty acid synthases (FAS), and saxitoxin (STX) biosynthesis genes (<i>sxt</i>). We identified 95, 117, and 39 PKS-related transcripts in <i>P. apiculatus</i>, <i>P. bipes</i>, and <i>C. furcoides</i>, respectively, which include single-domain PKS, multi-domain PKS, and hybrid NRPS/PKS. Phylogenetic analysis revealed a novel clade of ketosynthase (KS) domains unique to freshwater dinoflagellates, suggesting species-specific diversification. Conserved catalytic residues were found in type II FAS genes across both freshwater and marine taxa. Although core STX biosynthesis genes were absent in all analyzed species, several STX-associated transcripts, including <i>sxtA4</i>, <i>sxtU</i>,<i> sxtS</i>,<i> sxtD</i>,<i> sxtH/T</i>, and <i>sxtI</i>, were identified. Phylogenetic analysis of the sxtA4 domain revealed that freshwater dinoflagellate sequences form a distinct clade from those of toxic marine dinoflagellates and cyanobacteria while retaining conserved active sites, suggesting potential functional variation. These findings reveal unique PKS and STX gene features in freshwater dinoflagellates, highlighting their previously unrecognized biosynthetic diversity, ecological roles, and biotechnological potential.</p>