Mesophilic Bioreactors are operated at mesophilic temperature of 28 to 32°C. The phylogenetic diversity of these bioreactors are studied by two complementary methods like PCR-DGGE of rRNA gene as well as cloning and determination of the nucleotide sequence of nearly complete rRNA genes amplified by PCR. Mesophilic bioreactors are used to treat pharmaceutical wastewater that refers to the presence of clones that have the closest phylogenetic affiliation to the proteobacterium HMD 444 in the bioreactors. The organism like mazeii is a key element for mesophilic digestion. The mesophilic reactors are included at least six bacterial divisions, including cytophaga-flavobacterium-bacteroides, synergistes, planctomycetes, low-G1C gram-positives, holophaga-acidobacterium and proteobacteria.