The study of how population structure and persistence are shaped by attributes of species and the environment is a central scientific pursuit in ecology and conservation. In this dissertation, I explore four themes central to this pursuit. First, I examined the extent to which species' ecological strategies - their life histories, biology, and behavior - predict patterns and drivers of population connectivity. This research represents a critical step in evaluating the potential of multi-taxa inference in landscape genetics. I examined a suite of hypothesized relationships between genetic connectivity and landscape connectivity for three desert anuran species and found a positive relationship between population differentiation and water dependency, e.g. longer larval development periods and site fidelity for reliable water sources. I also found that aquatic connectivity is important across all species, particularly when considered with topography (slope). Second, I built upon the work of my first chapter and proposed more general traits-based frameworks to enhance the utility of landscape genetics in multispecies conservation. I proposed guiding principles for the formal development, testing, and generalization of traits-based frameworks to advance the utility, efficiency, and effectiveness of genetic inference in contemporary ecology and conservation. Third, I employed population genetic techniques to examine the population structure, diversity, and connectivity of Hyla wrightorum, an anuran native to the southwestern United States and Mexico. Hyla wrightorum exists as a Distinct Population Segment (DPS) in the Huachuca Mountains and Canelo Hills of southeastern Arizona, USA. Due to concerns about declining observations of the species within the DPS, its small geographic and isolated extent within the Huachuca Mountains and Canelo Hills, and presumably small population sizes, the DPS is currently a candidate for federal protection under the Endangered Species Act. I found evidence of larger than expected effective population sizes, significant genetic differentiation between populations, and an isolation-by-distance pattern among populations. These results suggest that the DPS may be less vulnerable to extirpation than previously expected, but some small effective population sizes and the limited geographic extent of the DPS justify current concern for the persistence of this DPS. Finally, I used a spatially-explicit individual based model to simulate the response of the Arizona Treefrog (Hyla wrightorum) to reductions in breeding habitat availability in an isolated portion of its range. I found that reductions in breeding habitat resulted in population declines, with the greatest population declines for H. wrightorum associated with both a reduction in breeding habitat availability and recruitment failure. Reduced breeding habitat also resulted in increased synchrony and decreased variability through time, which likely indicates a transition from a metapopulation to isolated populations. Taken together, the four chapters of this dissertation advance the use of landscape and population genetics in multispecies conservation, and they will contribute directly to the conservation of dryland aquatic species.