In order to provide information for the HAB toxin synthesis mechanism and explore the role of polyketide synthase in the synthesis of HABs toxins, potential polyketide synthase (PKS) gene in Prorocentrum lima was amplified by PCR using degenerate primers. The homology analysis of the PKS gene in related species was conducted and phylogenetic tree was constructed using software of DNAStar and DNAMAN. The expression of PKS in P. lima was determined using reverse transcriptase polymerase chain reaction (RT-PCR). Multiple approaches including amplification of polyadenylate RNA, resistance to methylation-sensitive restriction enzymes, Southern blotting, and isolation of bacteria from cultures were performed to eliminate the possibility of PKS in associate bacteria. Results showed that type I polyketide synthase may be present in Prorocentrum lima, which grouped strongly with P. mican. High level expression of PKS in Prorocentrum lima were observed. 18S rRNA and PKS gene were amplified successful by RT-PCR using Oligo(T). The analysis of 16S rRNA sequece showed 99% homology between bacteria from P. lima culture and marine actinomycete Pseudonocardia. However, PKS gene was not obtained by PCR and no expression of PKS was detected by RT-PCR in the bacteria. These results suggested that the PKS gene was P. lima originated but not bacteria. PKS might play an important role in the production of diarrheic shellfish poisoning toxins. The sequence of PKS has been accepted by GenBank (accession NO: EF521601).