Ribotyping analysis combining with denaturing gradient gel electrophoresis (DGGE) have been successfully used and described the biodiversity of microbes especially archaea from cattle manure. DGGE profiles of the archaea methanogens based on culture-independent showed variation patterns from early mesophilic to maturation phases. During early mesophilic to thermophilic phases the DGGE bands at the upper part of the gel showed less variation. Meanwhile at the thermophilic phases, the upper bands were disappeared. While at the end of thermophilic phase the DGGE bands showed more variation compared to that in the early of mesophilic phase. However, in the maturation phase only four bands appeared on the middle and bottom of the gel. Detail analysis by comparing the sequence of 16S rRNA gene fragments to the GenBank showed that all the bands were closed to Methanosaeta, uncultured archaeon, and Methanobrevibacter, which belonged to the phylum of Euryarchaeota. Phylogenetic analysis of the 16S rRNA gene sequences showed that all the bands belonged to Methanobacteriales and Methanosarcinales. 18 out of 25 DGGE bands showed that the bands are forming a new cluster at Euryarchaeota based on phylogenetic analysis, where 14 bands were closed to Methanobacteriales and 4 bands are part of Methanosarcinales. Most of Methanosarcinales order were found at thermophilic phase and Methanobacteriales were found in all phases. In addition the organisms were dominant order in both mesophilic and maturation phases.