SDS and Triton X-100 added at their critical micelle concentrations (CMCs), increased phenanthrene solubility in the presence of sediments and inhibited phenanthrene biodegradation. Triton X-100 caused more inhibition than SDS. 16S rDNA analyses revealed that both surfactants changed the microbial communities of phenanthrene-degrading cultures. Further, after the surfactant additions, parts of the microbial populations were not detected and methane production decreased. Surfactant applications, necessary to achieve actual CMCs, alter microbial community structure and diminish methanogenic activity under anaerobic conditions. We propose that this change may be related to the inhibitory effects of SDS and Triton X-100 on phenanthrene biodegradation under methanogenic conditions.