DNA encoding antibiotic resistance genes (ARG) has recently been established as an emerging contaminant. In addition to imparting drug resistance to bacteria, ARG also have good potential as bioindicators of the impacts of antibiotic pharmaceuticals in the environment. ARG have been found in a wide cross-section of environmental compartments, including: wastewater treatment plant effluent, biosolids, agricultural lagoons, groundwater, surface water, and drinking water. In this study, the relationship between urban versus agricultural land-use on the relative concentrations of ARG in the Cache La-Poudre (Poudre) River watershed in northern Colorado is explored. Two tetracycline ARG (tetW and tetO) and two sulfonamide ARG (sulI and sulII) were quantified in river sediments using real-time quantitative polymerase chain reaction (Q-PCR).  It was found that both urban and agriculturally impacted zones of the river had elevated levels of ARG compared to a pristine control site at the headwaters of the river in the Rocky Mountains.  Current efforts are now focused on developing and applying ARG fingerprinting techniques using capillary electrophoresis single strand conformation polymorphism (CE-SSCP).  This will aid efforts in tracking the fate and transport of ARG in the environment in order to develop effective strategies for containing environmental resistance and protecting human health.  Suitable ARG treatment approaches may then be developed and applied to prevent the dissemination of ARG in the environment.  The results of recent research on two options for achieving this through on-farm lagoon treatment and composting will be presented.