Environmental factors can limit the distribution of organisms if they are not able to respond through phenotypic plasticity or local adaptation. Batrachochytrium dendrobatidis (Bd) is a broadly distributed pathogen, which shows spatially patterned genotypic and phenotypic variation; however, information on the functional consequences of this variation on disease dynamics in natural hosts is limited. We genotyped and quantified variation in Bd phenotypes across an elevational gradient and quantified host infection dynamics at each site. All Bd strains were members of the global panzootic lineage yet differed in phenotype. We hypothesize that this phenotypic variance results from adaptive processes due to the interaction between pathogen, hosts, and environment. We detected a correlation between zoospore and zoosporangia sizes and a positive association between zoosporangia size and Bd prevalence. Given that Bd phenotype predicted disease status in our wild populations, we developed an index to identify critical environments where the fungus could be more deleterious. © 2015 Elsevier Ltd and The British Mycological Society.20 1521