Electron donor supplements are commonly used to enhance the degradation of soil organochlorine contaminants. Dynamic processes of pentachlorophenol (PCP) dechlorination induced by adding electron donors are well known, however, their effects on the microbial communities providing these activities are only poorly understood. In this study, the effect of three electron donors (citrate, glucose and lactate) on the rate and extend of PCP dechlorination, and on the prokaryotic (bacterial and archaeal) community structure was investigated. The addition of citrate or lactate increased reductive dechlorinated rates of PCP, whereas the addition of glucose decreased the rates. High-throughput sequencing analysis of microbial communities in the microcosms found that Pseudomonas, Hydrogenophaga, Clostridium, Dendrosporobacter, Burkholderiaceae, and Fervidicella were the main microorganisms in treatments without electron donor additives, and treatments with citrate or lactate. With the glucose treatment, Clostridium, Fervidicella, Sedimentibacter and Acetivibrio were observed to be the main genera. The addition of citrate and lactate enhanced the population of bacteria with a known potential of reductive dechlorination, with the consequence of accelerating the dechlorination of PCP. However, the addition of glucose stimulated the activities of the organisms that can utilize glucose but cannot dechlorinate PCP. These findings indicate the critical role of different electron donors in stimulating different microorganisms and suggest the appropriate selection of electron donors for accelerating the bioremediation of PCP-contaminated soils.