Habitat loss and chytridiomycosis (a disease caused by the chytrid fungus Batrachochytrium dendrobatidis - Bd) are major drivers of amphibian declines worldwide. Understanding how their independent and interactive effects lead to amphibian declines is critical for biodiversity conservation. For my doctoral research, I (1) developed a novel integrative approach for systematic conservation planning for tropical amphibians facing negative impacts of accelerated habitat loss, (2) quantified the influence of deforestation on the risk of chytridiomycosis, and (3) through a combination of field surveys and laboratory-controlled experiments, identified abiotic and biotic mechanisms that link deforestation to shifts in disease dynamics. Chapter 1 evaluates different scenarios of systematic conservation planning for Brazilian amphibians, integrating data on species life-history and ecologically relevant spatial metrics of deforestation and landscape configuration. Chapter 2 describes a paradoxical negative relationship between habitat loss and the risk of chytridiomycosis in amphibian populations from Costa Rica, Brazil, and Australia, laying the foundation for chapters 3, 4, and 5, which focus on mechanisms by which deforestation alters disease dynamics. Chapter 3 describes cascading effects of deforestation linking reduction in canopy cover to microclimatic shifts, which affect both Bd prevalence and infection intensity. Chapter 4 experimentally tests and finds support for the 'dilution effect' hypothesis, which predicts an inverse relationship between host diversity and disease. In Chapter 5, I show that temperate amphibian communities with higher population densities at pristine closed-canopy sites carry higher Bd loads due to density-dependent transmission. In contrast, tropical amphibian communities commonly found in pristine forests carry lower Bd infection loads than those in disturbed habitats, presumably due to their host species composition. These results combined highlight that deforestation shifts abiotic and biotic factors, which in turn can either increase or decrease disease risk and impact conservation efforts in amphibians. My dissertation work has important analytical and theoretical implications for the field of disease ecology and the management of amphibians facing the dual negative impacts of habitat loss and chytridiomycosis.