[Objective] We identified polyketide synthase (PKS) genes from mangrove soil. [Methods] Degenerate PCR primers were used to amplify ketosynthase (KS) domains associated with type I and II PKS genes from DNA of soil samples derived from the Qinglan Harbor (Hainan, China). The molecular diversity and phylogeny of type I and II PKS genes were analyzed by PCR-RFLP based cloning approach. [Results] A total of 72 clones and 51 OTUs were obtained, there was no dominant OTU and 37 OTUs were from single clone. Twenty-six clones of different OTUs were sequenced and the DNA sequences were translated into amino acid (AA) sequences. All identified KS domains showed the identities at AA level to their closest matches in GenBank at less than 85%. Phylogenetic analysis of these sequences indicated that the identified ketosynthase (KS) domains were clustered with those from diverse bacterial group, including Cyanobacteria, Proteobacteria, Firmicutes, Actinobacteria and some uncultured bacteria. A total of 55 clones containing Type II PKS gene KS domain DNA sequences were analyzed by PCR-RFLP. Only 25 OTUs were generated and there were two dominant OTUs which present more than 10% of clones in the clone library. [Conclusion] These results suggested the presence of diverse PKS I and PKS II genes in microorganisms from mangrove rhizosphere soil, and the diversity of PKS II gene is lower than the PKS I gene. Low KS domain sequence similarities indicated they possessed unique PKS I genes. Phylogeny deduced from the sequences of KS domains in PKS I genes showed that they distributed in different bacterial phyla.