Species and populations with low genetic diversity are at a higher risk of extinction because of an inability to adapt to threats such as environmental change. Human activities have drastically reduced the amount of habitat, the number of populations, and population connectivity of many species throughout the world. Fragmented populations can exist as isolated populations with no gene flow or as metapopulations - groups of discrete demes that maintain some level of gene flow. The Topeka shiner (Notropis topeka) is an endangered cyprinid native to the Midwestern United States. Topeka shiners have experienced drastic reductions in distribution due to stream alterations that have eliminated both instream and off-channel habitats, leaving smaller, more isolated populations throughout the range. Species with small isolated populations can suffer from low genetic diversity and lack of gene flow. A total of nine polymorphic microsatellite loci were used to asses genetic diversity, analyze population structure, compare migration rates across the range, and characterize metapopulation structure across the range of the Topeka shiner. Rangewide analysis of population structure revealed eight distinct populations with moderate levels of genetic diversity that can serve as management units for conservation. Estimates of historical and contemporary migration indicated that populations were more connected thousands of years ago whereas current populations have almost no gene flow between them. These results suggest habitat destruction has led to a reduction in genetic connectivity across the range of the Topeka shiner leaving the remaining populations geographically isolated. Analysis of genetic structure within the Rock River and Boone River basins indicated deviations from Hardy-Weinberg Equilibrium, significant genetic isolation by distance, and low but significant genetic differences between sites. These results suggest Topeka shiners in these basins are acting as metapopulations composed of discrete demes. Analysis of migration patterns indicate larger demes may be acting as potential populations sources that export individuals to other demes. Although Topeka shiner populations exhibit moderate levels of genetic diversity throughout the range, failure to correct the factors that led to a decline of this species will result to reduced diversity, leaving populations susceptible to stochastic events. Given the vast geographic distance between many populations, natural reestablishment is unlikely between these populations. Managers, therefore, should focus on preserving or improving genetic diversity within these populations. Improving the amount and distribution of quality habitat to will allow Topeka shiners metapopulations to expand and persist in within basins.