Microorganisms can cause detrimental effects in shale gas production, such as reservoir souring, plugging, equipment corrosion, and a decrease in hydrocarbon production volume and quality, thus representing a multi-billion-dollar problem. Prefracturing fluids, drilling mud, and impoundment water likely introduce deleterious microorganisms into shale gas reservoirs. Conditions within the reservoir generally select for halotolerant anaerobic microorganisms. Microbial abundance and diversity in flowback waters decrease shortly after hydraulic fracturing, with Clostridia, a class that includes spore-forming microorganisms, becoming dominant. The rapid microbial community successions observed suggest biocides are not fully effective, and more targeted treatment strategies are needed. At the impoundment level, microbial control strategies should consider biocide rotation, seasonal loading adjustments, and biocide pulse dosing. In shale plays where souring is common, stable 34 S/ 32 S isotope analysis to identify abiotic H 2 S is recommended to evaluate the merits of biocide application in treating reservoir souring. Overall, an improved understanding of the microbial ecology of shale gas reservoirs is needed to optimize microbial control, maximize well productivity, and reduce environmental and financial burdens associated with the ad hoc misuse and overuse of biocides.