<p>Peripheral and disjunct populations are often the result of historic geological changes in the landscape and because of the long temporal span of colonization or vicariance, they are often genetically distinct and, when occupying small areas, vulnerable to population declines. In freshwater fishes, such populations are very susceptible to habitat destruction and environmental changes that could hasten extirpation. Because these populations are both geographically disjunct and genetically distinct from other populations, natural recolonization may be unlikely, and, because of the potential differences in the environment, human-mediated reintroductions may subsequently fail. Understanding the metapopulation genetic variation of those populations is critical for management efforts. Here, we assess the genomic variation and demographic history of the Ironcolor Shiner (<i>Alburnops chalybaeus</i>) with emphasis on the peripheral and disjunct populations. We find that the phylogeny of the species supports the hypothesis of an ancestral range in the southeast, while two independent lineages subsequently dispersed along the Atlantic coastal drainages and the Mississippi basin. We also inferred that genetically isolated, peripheral populations in Illinois and New Jersey have experienced geologically recent post-glacial population declines following glaciation consistent with their recent isolation. These findings imply the need for separate management of potential evolutionary significant units across the range of Ironcolor Shiner, as this broadly distributed species represents a series of isolated, disjunct populations. While many species may not be federally listed, extirpation of their peripheral populations is a key conservation issues requiring further attention.</p>