It is widely believed that biochar plays an important role in sequestrating pollutants in soil. The impacts of biochar on soil microbial community structure, and consequently on the environmental fate of soil pollutants, however, remains poorly understood. In this study, rape-straw derived biochar was used to investigate how biochar amendment affected microbial communities and pentachlorophenol (PCP) transformation in a paddy soil under anoxic conditions. PCP sorption and transformation and HCl-extractable Fe(II) generation were significantly enhanced in biochar amended soils. The results showed that the enhanced transferred extracellular electron in biochar amended soils promoted the PCP transformation while biochar supplement promoted the growth and metabolism of microorganisms in the soil. The relative abundance of dominant microbial population was bearing on biochar dosages in the soil. In addition, quantitative real-time PCR results illustrated that biochar acted as a growth stimulant for iron(III)-reducing and dechlorinating bacteria, which consequently promoted PCP biotransformation. Our findings indicated that rape-straw derived biochar may be an important agent for activating the soil functional microbial communities and can be used to environmental-friendly accelerate the remediation of PCP contaminated paddy soils.