Over the last 30 years animal production has become increasingly intensive with fewer operations producing larger numbers of animals. As a consequence, the animal waste is produced and maintained in fewer facilities and in greater concentrations. The manure is a valuable resource for crop fertilization and soil conditioning. However, there are also significant concerns associated with the handling of increasing volumes of animal wastes which pose a threat to air, soil and water resources. With the national livestock inventory steadily increasing, there is greater need to improve waste storage and handling to maximize the benefits while mitigating any negative consequences of animal waste utilization. Microorganisms are central to both the beneficial (nutrient cycling, biogas production) and detrimental (i.e., excess nutrients, pathogens and pharmaceutically active compounds) aspects of animal manures. Therefore, characterization of microbial ecosystems associated with livestock manure and storage systems should aid in developing better means for management and usage of waste materials. Here we describe research conducted to describe microbial communities associated with livestock wastes (swine, poultry and beef) and how management practices impact the structure and function of important microbial groups. Contaminant distribution, pathogen survival and the effect of management practices on important microbial functional groups (i.e., nitrogen cycling, ammonia and methane production) will be discussed. A better understanding of microbial communities associated with manures should aid in development of management practices that permit sustainable use of manures in order to protect soil, water and air quality.