The microbial community of a 2,4-dinitrophenol-digesting reactor was investigated using different molecular biological techniques based on 16S rDNA gene sequences. A PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the bacterial community in the reactor showed that one strong and five minor bands were observed in the DGGE profile. The results of excising and sequencing DGGE bands suggested that members of Rhodococcus, Nocardioides, and Nitrospira species were present in the reactor. Partial sequencing of cloned 16S rDNAs revealed diversity among the six main divisions-the alpha, delta subclasses of Proteobacteria, Nitrospira, Cytophaga/Flexibacter/Bacteroides, Verrucomicrobia, and Actinobacteria-in the reactor. Two cloned sequence types were not closely affiliated with any described bacterial divisions. The isolation and phylogenetic analysis of 2,4-DNP-degrading bacteria from the reactor revealed that isolated strains were classified into two types of bacteria having different 16S rDNA sequences.' One of these strain types was identified as a relative of Rhodococcus koreensis, and the other was identified as a relative of Nocardioides simplex FJ21 -A.