To determine whether the chytrid fungus Batrachochytrium dendrobatidis (Bd) found on the hellbender Cryptobranchus alleganiensis in the southern US is endemic or exotic, we identified the genetic type of this fungus using partial DNA sequences of the internal transcribed spacer (ITS) region. We identified 3 genetic types, which are found on Japanese amphibians other than the Japanese giant salamander Andrias japonicus, a species that belongs to the same family (Cryptobranchidae) as hellbenders. The fungus collected from hellbenders exhibited low genetic diversity and matched the common Bd genetic types which have been detected from around the world. These results support that the chytrid fungus on the hellbender is a novel pathogen, as proposed by previous studies. Although we have not observed disease symptoms directly linked to this fungus on this endangered salamander, further evaluation of the influence of this exotic fungus on this species is warranted.