The knowledge regarding characterization of PCB dechlorinating microbial community of the extremely high PCB-contaminated Ralston Street Sewage Lagoon TSCA site in Gary, Indiana and the residual paper mills along the Kalamazoo floodplain Superfund site is substantially infinitesimal. Therefore, effective PCB-dechlorinating microbes Catonella sp. and Paenibacillus alginolyticus in these environmental “toxic” reservoirs (in alfalfa rhizospheres), would provide the needed alternative bioremedial strategy. Soil samples from control and experimental PCB-contaminated field sites were evaluated for a comparative assessment to attain the phylotypes of the variant microbial communities in the presence and absence of alfalfa. Recent molecular applications in 16S rRNA microbial community profiling refer to T-RFLP (Terminal Restriction Fragment Length Polymorphism) as a high-throughput technique, where molecular approaches having the least amount of environmental disruption and hazard, yield swift, accurate results with more identifiable species. Purified fluorescently-labeled amplicons from PCR reactions were digested with diagnostic restriction enzymes in separate reactions to distinguish representatives of the total bacterial community. A CEQ 8000 Genetic Analyzer was used to identify fragments for community structure analysis. The Ribosomal Database Project (RDP) was used for the 16S rRNA comparative microbial community designations, identifying the specific phyla Actinobacteria, Bacteroidetes, Deinococcus/Thermus, Firmicutes, Proteobacteria, and more. Use of restriction enzymes, Hha, MspI and RsaI produced the maximum number of peaks of varying fragment sizes (lengths in base pairs). GC-MS analyses show that PCB-degrading microbes in high PCB sewage sludge are enhanced by alfalfa plant. The expected environmental benefit would be to use the modified T-RFLP profiles to indicate the most effective PCB dechlorinator(s), while capturing two consequential commodities, time and ecological safety.