The dinoflagellate Karenia brevis (C. C. Davis) Gert Hansen et Moestrup produces a suite of brevetoxins, potent neurotoxins that have adverse effects on marine animal and human health. Brevetoxins are polyketides proposed to be synthesized by polyketide synthases (PKSs), and genes for type I PKSs have been predicted by PCR and transcript analysis. However, the full-length transcripts in K. brevis predict an unusual protein structure for type I PKS in that individual transcripts encode for single catalytic domains. In this study, we developed peptide antibodies to in silico translated transcripts for two PKS proteins to characterize their expression and localization. Immunoreactive proteins identified by Western blotting at 40 kDa (KR domain) and 100 kDa (KS domain) are consistent with the sizes predicted by the full-length transcripts. Immunolocalization and Western blot analysis indicate that these PKSs are associated with the chloroplasts. In order to establish evidence for a role in brevetoxin biosynthesis, PKS transcript and protein levels were examined in a “nontoxic”K. brevis substrain and its parental toxic isolate, K. brevis Wilson. DNA microarray analysis of the global transcript profiles in the “nontoxic” isolate showed that ∼7% of transcripts were differentially expressed, including photosystem genes; however, no difference was observed in PKS transcript abundance. By contrast, KS domain proteins were 55%–70% less abundant in “nontoxic”K. brevis cultures compared to toxic cultures. This finding suggests that K. brevis PKS expression is regulated posttranscriptionally, like many other processes in dinoflagellates. Further, the decrease in PKS protein abundance in the “nontoxic” cultures provides correlative evidence for their involvement in brevetoxin biosynthesis.