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Secretive species are difficult to study and often of conservation concern, as exemplified by the Eastern Hellbender (Cryptobranchus alleganiensis). Traditional methods for sampling Hellbenders involves moving rocks, which damages essential habitat. Use and installation of artificial shelters has made studying Hellbenders less dangerous for the animal and less disruptive to stream habitat; however, researchers using shelters generally capture occupying animals to identify them. We tested the ability of a submersible portable Passive Integrated Transponder (PIT) antenna to accurately detect PIT-tagged Hellbenders in shelters. We tested the effects of the presence and depth of cover rocks on top of shelters, PIT tag location within the shelter, and tag orientation on detection efficiency of Hellbenders. For the 32 shelters occupied by a tagged individual with cover rocks in place, the scanner accurately detected 31% of the animals versus 88% when cover rocks were removed. The detection efficiency of the scanner dropped below 50% once cover rock depth exceeded 11 cm. Tags placed near the interface of the entrance tunnel and chamber, or along the chamber walls, had higher detection efficiencies than those in other locations within the shelter. Vertically oriented tags were 18% more likely to be detected than horizontally oriented tags. Our study demonstrates that while this technology has certain limitations, it shows potent