The fungal pathogen Batrachochytrium dendrobatidis (Bd) causes the disease chytridiomycosis, which is responsible for many amphibian declines worldwide. The determinants of Bd’s high virulence across a wide range of amphibian species are not well understood but include environmental factors, host responses to infection, and pathogenicity of Bd. Because there are clear differences among Bd isolates, genetic profiling of multiple strains is currently in progress. However, genetic analyses alone may not provide a functional explanation for differential virulence among strains. I aimed to quantify phenotypic traits, such as zoospores densities, that are important for disease development. Among the three isolates tested, zoospore densities were highest in GibboRiver-L.lesueuri-00-LB-P24, an isolate originally collected from a Litoria lesueuri tadpole and highly virulent in infection experiments. Because characterizing differences among isolates is central to understanding Bd pathogenicity, integrating genetic work with the phenotypic profiling methods provided in this study will offer insights into chytridiomycosis and may be important for amphibian conservation.