The bacterial diversity in the Alternate-flow Biological Reactor (ABR) of pharmaceutical wastewater which was of high efficiency for the CODcr, nitrogen, petroleum and other especial pollutants was studied by the 16S rDNA clone library. These sequences were compared with 16S rDNA sequences deposited in public databases of NCBI. The results indicated that the bacterial diversity was high in the ABR. The dominant bacterial community in the ABR was Proteobacteria which accounted for 78.6%. The bacterial community succession were as follows: Alphaproteobacteria (39.8%), Betaproteobacteria (23.5%), Gammaproteobacteria (14.3%), Chlorobi1 (6.3%), Firmicutes (4.1%), Flavobacteria (1.0%) and Deltaproteobacteria (1.0%). Phylogenetic tree of the new sequences and the 16S rDNA gene sequences of various bacteria was obtained by Vector NTI Suite 6.0 software.