Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, which has caused devastating amphibian population declines. Little is known about the biology of Bd on hosts, and techniques for diagnosing it on living and preserved animals are still evolving. We investigated the spatial distribution of Bd on the integument of naturally infected Australian hylid frogs Litoria genimaculata at 4 rain forest localities in northern Queensland, Australia. We collected 555 samples by swabbing 111 individuals on 5 regions of the body (back, abdomen, legs, forefeet and hindfeet). Numbers of zoospore equivalents on each body region were quantified using a real-time TaqMan PCR assay. The intensity of infection differed significantly among body regions and this pattern of differences differed among sampling localities. The lightest infections were usually centered on the abdomen, while heavier infections were concentrated on the legs and feet. The back was always either lightly infected or uninfected. Many frogs with light infections had positive PCR results only for the abdomen or the legs. We compared swabs taken from the legs and abdomen and found that they provided similar sensitivity to detect infections, but using both regions together led to greater sensitivity than either region alone. Because swabbing may transfer zoospores from infected to uninfected regions within individuals, we suggest that the best procedure for all species is to employ separate swabs for each body region. If that cannot be done, swabbing patterns that minimize potential harm should be determined for each species, and possibly each class of individuals (e.g. males, females, juveniles) within species, by examining the distribution of infection among body parts in naturally infected individuals.