The successful application of co-immobilized aerobic-anaerobic biomass under limited aeration in wastewater treatment systems would eliminate the problems associated with the intermediates mono-chlorophenol (MCP) and di-chlorophenol(DCP) accumulations. With low initial pentachlorophenol (PCP) concentration, all PCP could be completely removed under oxygen-limited strict anaerobic conditions, and the removal efficiencies with different initial headspace oxygen percentage (IHOP) were not obviously different from each other. While at high initial PCP concentration, under strictly anaerobic conditions PCP and their intermediates were clearly higher than that under other conditions, and produced obvious accumulation, the highest PCP reduction was achieved by the system receiving 30 IHOP, oxygen-limited system also exhibited lower residual TOC concentration and lower concentration of metabolic intermediates MCP and DCP. These results suggested that under strictly anaerobic condition the reductive dechlorination of low chlorinated compounds became rate limiting in the reductive dechlorination pathway, less chlorinated compounds be more amenable to aerobic degradation, and the aerobes of outer layers could function under limited oxygen. The co-immobilized aerobic-anaerobic biomass for methanogenesis under limited-aeration for chlorophenol degradation might be an attractive and efficient alternative for the sequential anaerobic/aerobic system to achieve mineralization of a broad range of recalcitrance highly chlorinated organics and low final TOC concentrations.