Understanding the ecological mechanisms responsible for patterns of spatial genetic structure and diversity is a central issue to evolutionary ecology and biodiversity conservation. The Anthropocene has seen a mass extinction only previously observed through geological records, and freshwater fishes of North America have not been spared owing to large-scale modification of freshwater habitats and introduction of nonnative species. Concomitant with reduced numbers of species is a rapid reduction in genetic diversity within species; this diversity that is required for species to adapt to rapidly changing environments of human dominated landscapes. However, understanding why species exhibit different patterns of spatial genetic structure and genetic diversity requires substantial ecological data and knowledge of species life histories. This body of research incorporates both ecological and genetic data to address key issues related to the conservation of native fishes of the upper Gila River, NM, USA, and evaluates how differences in ecology among species influences their evolutionary trajectories (i.e., genetic diversity and structuring). Chapter 1 adopted a conservation genetics approach to evaluate the genetic health and long-term maintenance of genetic diversity of three imperiled species protected by New Mexico State and United States Federal laws. Estimates of contemporary effective size were low for these species, as were estimates of genetic structure (all species FST \u3c 0.025) suggesting moderate to high gene flow for all species. Chapter 2 broadened the scope of focal species by including most of the fish community and increasing life history variation to evaluate how dispersal and life history influence patterns of genetic structure within a shared riverscape (i.e., attributes of a landscape specifically related to networks of streams and rivers). A key result was that genetic patterns were highly variable among species and related to life history and abundance. Across species, overall genetic differentiation (FST) was not strongly predicted by species traits, but fecundity was negatively associated with effect of distance on genetic structure (measured by Mantel\u27s r). Chapter 3 examined the relationship between metapopulation processes and species evolutionary trajectories. Metapopulation genetic effective size was reduced by temporal instability (extirpation/recolonization), but high abundance appeared to counter balance effects of temporal instability. These results indicate that ecological trade-offs related to life-history strategies (e.g., fecundity, body size, parental investment, etc.) also influence individual species\u27 evolutionary responses (i.e., genetic diversity and differentiation) to landscape factors and threats to persistence
