Abstract:Microbial diversity of composting of agriculture organic wastes (AOW) and municipal domestic waste (MDW) in the thermophilic (T) phase was analysed by Polymerase Chain Reaction (PCR) combined with constructing of clone library. The polymerase chain reaction-amplified 16S rDNA and 18S rDNA fragments with universal eubacterial primers(27F, 1495R) and fungal primers (EF4, Fung5) were subjected to constructing of clone library, and the results of clone library indicated: there were 18 OTUs and 21 OTUs in the 16S rDNA clone library of AOW and MDW composting sample, and they belonged to 14 and 15 different genuses respectively; in the 18S rDNA clone library of AOW and MDW composting sample, there were 8 OTUs and 9 OTUs, and they belonged to 8 and 9 different genuses respectively. The doninent microbes in the T phase of composting of AOW were related to Bacillus megaterium, Rhizobium sp., Phanerochaete chrysosporium, Penicillium sp., and the doninent microorganisms in the T phase of composting of MDW were related to Bacillus megaterium, Azospirillum sp. and Phanerochaete chrysosporium.