The microbial communities in a two-stage anaerobic digestion process treating olive mill “solid” residues were studied by molecular identification techniques. The microbial species identification in the hydrolytic-acidogenic step and in the methanogenic step was carried out by polymerase chain reaction amplification of 16S ribosomal RNA genes, denaturing gradient gel electrophoresis, cloning, and sequencing. This study revealed that Firmicutes (from 31.1 to 61.1 %, average 42.1 %) mainly represented by Clostridiales, and the Chloroflexi (from 29.4 to 53.3 %, average 47.35 %) were the most abundant species for the hydrolytic-acidogenic reactor. Other microorganisms such as Gamma-Proteobacteria (Pseudomonas species as the major representative; from 3.9 to 9.7 %; average 5.7 %), Actinobacteria (from 1.0 to 10.2 %; average 4.6 %) and Bacteroidetes (from 1.1 to 3.1 %; average 1.7 %) were also detected. The methanogenic communities detected in the methanogenic reactor were mainly represented by members of the obligate acetotrophic methanogenic genus Methanosaeta. Methanosaeta was the crucial Archaea to obtain a high methane yield in the methanogenic stage.