Canaan Valley, an unusual, high-elevation bowl in the Mid-Atlantic region, is a headwater basin of the upper Blackwater River. Because of its unique geological and topographical setting, many plant and animal species, as well as several plant communities that are considered to be rare in West Virginia, are found in the Blackwater River watershed. In this paper, I describe the distribution of 72 rare species in general terms and discuss selected plant and animal species in greater detail. I also characterize potential threats and offer recommendations regarding the inventorying and monitoring of these rare taxa and natural communities.