New evidence suggests that the origins of the highly virulent strains of Batrachochytrium dendrobatidis may be more complex than originally thought. When the amphibian chytrid fungus first came onto the infectious disease scene, two hypotheses were proposed for its origins: the endemic and emerging pathogen hypotheses. The endemic pathogen hypothesis states that the amphibian declines arose from changes in an already present host-pathogen system, and predicts greater ancestral variation in chytrid lineages. The emerging pathogen hypothesis assumes that the amphibian declines arose from some novel strains of Bd and predicts more present day variation. However, this study did not significantly support either hypothesis, or even the hypothesis that Bd originated in Africa. In fact, a phylogeny constructed primarily using samples from North and South America suggested that a lineage of chytrid isolated from bullfrogs in Brazil might be the origin of the infection. This hypothesis is supported by the lack of major declines in many amphibian species from Brazil, despite the presence of Bd in some areas. The phylogeny also revealed greater diversity in the lineages of chytrid than was first thought, suggesting that more Bd samples should be collected for further genetic analyses. Understanding the genetic origins and variation of a pathogen like the amphibian chytrid fungus is important for learning how to combat it and predict its spread, since different strains may interact with the environment differently.