Previous research demonstrated that methanogenic cultures enriched from Baltimore Harbor (Baltimore, MD) sediments were able to degrade naphthalene and phenanthrene. In this report, the degradation activity was maintained through a sequential transfer without adding additional sediments and the established polycyclic aromatic hydrocarbon (PAH)-degrading methanogenic communities were characterized via comparative sequence analysis of clone libraries of 16S rRNA genes amplified using bacteria-specific and Archaea-specific primers. The phylogenetic analysis indicated that the addition of PAHs clearly shifted the structure of the methanogenic community and resulted in an increase in populations of species previously found in other hydrocarbon-degrading communities. Of particular interest is the fact that the dominant microbial population of the naphthalene cultures was different from that of the phenanthrene cultures, suggesting that different species are involved in the degradation. Finally, this information may lead to the identification and isolation of methanogenic populations that can degrade PAHs.