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The emerging pathogen, Batrachochytrium dendrobatidis (Bd), causes a fatal amphibian disease called chytridiomycosis, and has impacted amphibian biodiversity. Amphibian declines were first noticed in the 1970s and 1980s, decades before Bd was discovered (1998). In the Sierra Nevada mountains (California, USA), mass die-offs of Yosemite toads (Anaxyrus canorus) occurred in the late 1970s. In this study, we investigated the historical and contemporary Bd presence on A. canorus. We used a retrospective analysis to determine Bd presence/absence on 719 museum specimens collected between 1915 and 2005, and on an additional 1678 samples collected from live animals in the wild (2004–2012). For the 1678 contemporary dataset, we developed a statistical model to identify biotic and abiotic drivers of Bd infection likelihood. We found that: 1) Bd emerged coincident with historical declines; 2) Bd is currently widely distributed throughout the species range; 3) life stage, elevation, and precipitation regime were associated with Bd infection likelihood; and, 4) the juvenile life stage was the most highly infected, with some having Bd infection loads surpassing a mortality threshold identified in other species. In combination, our results suggest that Bd may have played a significant yet unrecognized role in the decline of A. canorus. Additionally, we find evidence that Bd may continue to affect survival and recruitment, depressing population growth and increasing extinction risk in remaining populations. These represent key insights for efforts to recover this species across its historical range and may also be important in hundreds of other species that declined before Bd was discovered. [ABSTRACT FROM AUTHOR]