Batrachochytrium dendrobatidis is a fungal pathogen that is receiving attention around the world for its role in amphibian declines. Study of its occurrence patterns is hampered by false negatives: the failure to detect the pathogen when it is present. Occupancy models are a useful but currently underutilized tool for analyzing detection data when the probability of detecting a species is <1. We use occupancy models to evaluate hypotheses concerning the occurrence and prevalence of B. dendrobatidis and discuss how this application differs from a conventional occupancy approach. We found that the probability of detecting the pathogen, conditional on presence of the pathogen in the anuran population, was related to amphibian development stage, day of the year, elevation, and human activities. Batrachochytrium dendrobatidis was found throughout our study area but was only estimated to occur in 53.4% of 78 populations of native amphibians and 66.4% of 40 populations of nonnative Rana catesbeiana tested. We found little evidence to support any spatial hypotheses concerning the probability that the pathogen occurs in a population, but did find evidence of some taxonomic variation. We discuss the interpretation of occupancy model parameters, when, unlike a conventional occupancy application, the number of potential samples or observations is finite.