Abstract: Biocontrol using antagonist agent is one of environment-friendly method of controlling bacterial leaf blight disease in rice field. Eight antagonistic bacteria against Xanthomonas oryzae pathovar oryzae as well as the causal bacterial leaf blight disease in rice, have been isolated from rice phyllosphere of Wonogiri and Sukoharjo Regency, Central Java, Indonesia, using dual plate method. The aims of this study were to identify molecularly of 16S rDNA and polyketide synthase (PKS) genes of antagonist bacteria. The PKS gene is recorded as one of antibiotic compounds class which encode the polyketide biosynthesis. The amplification of 16S rDNA gene was performed using 63f and 1387r primers, while PKS gene detection was performed using degKS2F.gc and degKSR5.gc primers. The nucleotide sequences of 16S rDNA and PKS genes was aligned using GenBank database and BLAST-N program from NCBI site was operated. The results showed that the eight isolates identity of SH2a, MO142, MO22g, MO34h, MO34i, MO34j, MO43a and MO63j were Pseudomonadaceae SH2a, Pantoea sp. MO142, Pantoea sp. MO22g, Erwinia sp. MO34h, Pantoea sp. MO34i, Pantoea sp. MO34j, Pantoea sp. MO43a and Pantoea sp. MO63j, respectively. Bacterial antagonists of PKS genes have similarities with the gene of nonribosomal peptide synthetase-polyketide synthase hybrid (cpbI) Lysobacter lactamgenus. This indicates that the antagonist mechanism of antagonist bacteria is antibiosis.