The abundance of the native, pelagic macroinvertebrate predator, Leptodora kindtii, is negatively correlated with the abundance of a new invasive competitor, Bythotrephes longimanus, in a small number of Canadian Shield lakes. However, we do not yet know if Bythotrephes is replacing Leptodora on a regional scale. We determined the distribution of both species in 166 lakes in the District of Muskoka, south-central Ontario, Canada-the watershed with the longest history and largest prevalence of Bythotrephes invasions in North America. The frequency of occurrence of Leptodora was substantially reduced (twofold) in the presence of Bythotrephes. We argue that Bythotrephes is responsible for this dramatic reduction in the frequency of occurrence of Leptodora. Lakes in which both species co-occurred could not be distinguished from invaded lakes without Leptodora, suggesting a pattern of species replacement at a watershed level. We believe this is the first account of the widespread replacement of a native, pelagic macroinvertebrate predator by Bythotrephes in North America, and it does not bode well for Leptodora given the rapid, ongoing spread of Bythotrephes.