Populations of the freshwater mussel genus Anodonta appear to be in a state of rapid decline in western North America, following a trend that unfortunately seems to be prevalent among these animals (Mollusca: Unionoida). Here we describe the patterns of molecular divergence and diversity among Anodonta populations in the Bonneville Basin, a large sub-basin of the Great Basin in western North America. Using amplified fragment length polymorphism (AFLP) analysis, we found a striking lack of nuclear diversity within some of these populations, along with a high degree of structuring among populations (FST = 0.61), suggesting post-Pleistocene isolation, due either to a long-term loss of hydrologic connectivity among populations or to more [...]