Recently emerged diseases in natural populations present novel problems for biodiversity conservation. Integrated approaches are needed to better understand disease-related threats, to mitigate these threats, and to assist population recovery. My dissertation research confronts the global amphibian biodiversity crisis. The recently emerged infectious disease chytridiomycosis, caused by the chytrid fungal pathogen Batrachochytrium dendrobatidis (Bd), infects hundreds of species around the world and is a major contributor to amphibian population declines. I use a multi-faceted approach to address critical issues of disease-caused amphibian declines. In this dissertation, I implement a novel methodology to gain insights on variability of host response to Bd (Chapter 2). Next, I analyze the spatial genetic structure of post-decline populations to aid conservation (Chapter 3). Finally, I examine the genetic underpinnings of pathogen attenuation - loss of virulence - using genomic sequencing (Chapter 4). First, I examine differential disease progression and host response in two related species (Chapter 2). Determining how different hosts respond to infection by a widespread pathogen is essential for understanding - and ultimately limiting - the devastating effects of emerging infectious diseases. Previous work demonstrated that susceptibility to chytridiomycosis is variable among species, but the mechanism(s) that underlie the difference between winners and losers remains a mystery. I used an integrative approach to analyze host response to infection in two related toad species that are thought to differ in susceptibility: the invasive Cane Toad (Bufo marinus) and the threatened Boreal Toad (Bufo boreas). With my results, I characterize the nature of differential susceptibility and compare host response using genome-wide gene expression analysis. The susceptible B. boreas exhibited high pathogen loads, loss in body weight, severe changes in the epidermis, and dramatic transcriptomic changes without a robust immune response. Conversely, the resistant B. marinus exhibited low pathogen loads, stable body weight, only mild disruption of the epidermis and relatively few changes in transcriptomic profile. Together our results show intrinsic differences in host response between related species, which are likely to be an important factor in explaining variation in response to a deadly emerging pathogen in wild populations. Second, I conducted a conservation genetics study of an endangered amphibian species in Yosemite National Park (Chapter 3). The most striking example of chytrid-associated population declines in North America is the mountain yellow-legged frog (Rana muscosa and Rana sierrae), including populations in Yosemite National Park. A clear picture of genetic structure and demography of remaining R. sierrae populations is critical to short-term management and conservation. I conducted a study to describe phylogeographic patterns of R. sierrae in Yosemite NP in collaboration with ecologists and park biologists. I utilized a recently developed method for multilocus amplicon sequencing that allows sequence data collection from a vast collection of swabs that contain low quantities of input DNA. My analysis of population genetic structure suggests that three genetic clusters occur in Yosemite NP with a significant signature of isolation by distance. This analysis of population genetic structure adds a critical component to the population recovery plan and will assist management strategies such as translocations, reintroductions, and monitoring. Third, I investigated the genomic changes associated with virulence attenuation in a lab-evolved Bd strain (Chapter 4). Despite recent efforts to characterize the diversity of Bd lineages, there are many questions that remain about the genetic underpinnings of pathogenicity. In a collaborative study, I take advantage of an accidental case of virulence reduction in a Bd strain that was lab passaged over many generations. I analyzed the genomic changes in strain samples cryo-archived before and after virulence attenuation. I found multiple patterns that may be linked to attenuation including decreases in chromosome copy number and mutations in putative virulence genes. These results contribute to the growing body of knowledge of how changes in pathogen genomes occur within a relatively short period of time, which has major implications for host-pathogen dynamics in natural systems. In conclusion, my dissertation provides important new contributions to the study of host-pathogen interactions with specific relevance to the fields of disease biology, conservation genetics, and pathogen evolution. Integrating genomic tools into a variety of experimental methods enabled not only valuable novel insights, but also opened up many new opportunities for further exploration of disease-caused amphibian declines using the generated genomic and computational resources.