Aquatic environmental DNA (eDNA) sampling is the collection of DNA released by a target species into streams, rivers, ponds, lakes, and wetlands. Detection of stream fish with eDNA can be remarkably sensitive—100% detection efficiency of target species has been achieved despite order-of-magnitude changes in stream discharge (Jane et al. 2015). Field experiments indicate that detection probability of a single trout in 100 m of stream exceeds 85%, an efficiency several-fold better than single-pass electrofishing (Wilcox et al. 2016). The simplicity and expedience of sample collection coupled with the potential for accurate estimates of species presence has led to widespread interest in this technique. At the National Genomics Center for Wildlife and Fish Conservation (NGC), scientists have been at the forefront of investigating and applying eDNA sampling for aquatic species, including developing the first reliable eDNA assay for salmonid fish species, the first that distinguishes bull trout from other species of char (Wilcox et al. 2013, 2014), and the first that distinguishes among subspecies of cutthroat trout (Wilcox et al. 2015a). The papers and other contributions by the NGC are detailed below. For a broader perspective on the burgeoning literature on eDNA sampling, please see the eDNA reference page maintained at Washington State University.