The modular polyketide synthase(PKS) and nonribosomal peptide synthetase(NRPS) were found to be involved in natural product synthesis in many microorganisms. Study on their diversities in natural environment may provide important ecological insights besides opportunities for antibacterial drugs development. The phylogenetic analysis of amino acid(AA) sequences indicated that the identified ketosynthase(KS) domains were clustered with those from diverse bacterial groups, including Cyanobaeteria, Proteobaeteria and some uncultured symbiotic bacteria. The NRPS included Cyanobaeteria and Proteobaeteria. One new branch belonging to hybrid PKS/NRPS enzyme complexes and five independent clades were found on the phylogenetic tree. These results revealed the great diversity and novelty of both PKS and NRPS genes from Mila Mountain in Tibetan Plateau.