Diversification rates among stream fishes are likely governed by geographical factors that impact connectivity among and between stream systems. Herein we investigate rates of diversification within species of River Chubs, Nocomis, a monophyletic group of stream fishes distributed throughout the drainage basins of the Mississippi River, Atlantic Slope and Gulf Coast. We used nucleotide sequences of two protein-coding nuclear genes (IRBP and rhodopsin) and one mitochondrial gene (cytochrome b) to generate a phylogenetic hypothesis of population-level relationships within and among species. Results of molecular analyses suggest that morphological and meristic treatments of Nocomis have underestimated species diversity within the group. Tree-based Bayesian methods and diversification statistics were implemented to model the rate of evolutionary change along lineages and estimate divergence dates among phylogroups. Significantly elevated rates of cladogenesis are observed among coastally distributed populations 2-3. million. years before present. This period was dominated by dramatic sea level fluctuations that suggest a period of climatic instability. Climatic instability and other factors may have driven the burst of rapid diversification observed in Nocomis. Results generated in this study reinforce faunistic and geologic arguments for the hypothesized existence of extinct rivers, such as White's River and the Appalachian River.