Despite a long history of anthropogenic contamination of Lake Erie sediments, little work has been done to understand the potential for PAH biodegradation by indigenous microbial communities. Pyrene-degrading Mycobacterium are prevalent in many polycyclic aromatic hydrocarbon (PAH)-contaminated freshwater sediments, and are of interest for their ability to degrade environmentally recalcitrant high molecular weight PAHs. This work tested the hypothesis that pyrene-degrading mycobacteria are prevalent in Lake Erie; an additional aim was to gain a baseline picture of the sediment microbial communities through sequencing a 16S rDNA clone library. Biodegradation potential of Lake Erie Mycobacterium populations was assessed through quantification of pyrene dioxygenase genes (nidA) and mycobacteria 16S rDNA genes using quantitative real time PCR. nidA was detected at all seven sampling sites across Lake Erie, with abundances ranging from 2.09 to 70.4 x 10(6) copies per gram sediment, with highest abundances at the most PAH-contaminated site (Cleveland Harbor). This is in contrastto naphthalene dioxygenase genes commonly used as biomarkers of PAH degradation: nahAc (from gamma-proteobacteria) was not detected anywhere, and nagAc (from beta-proteobacteria) was detected only in Cleveland Harbor, despite dominance by proteobacteria in Lake Erie sediment 16S rDNA clone libraries (>50% of clones). The prevalence of Mycobacterium nidA genotypes corroborated previous studies indicating that PAH-degrading mycobacteria have a cosmopolitan distribution and suggests they play an important but overlooked role in natural attenuation and cycling of PAHs in Lake Erie.