Hellbender salamander (Cryptobranchus alleganiensis) populations have received considerable attention over the last few decades and recent studies show declines. We compared C. alleganiensis populations and habitat characteristics of the Little River (LR) in the Great Smoky Mountains National Park (GSMNP) of Tennessee, with those of the North Fork of the White River (NFWR), Missouri. We also compared the results of two different sampling methods for obtaining small individuals < 20 cm total length (TL) and gilled larvae. There was no significant difference in the frequency of larvae and adults in LR. There were highly significant differences in the frequency of larvae and adults in the NFWR population and in the proportion of larvae and adults between LR and NFWR. The stream bottom substrate, especially the deep gravel beds of the NFWR, provided a more secure larval habitat than in the LR. We believe this secure larval habitat was a major factor in maintaining large adult populations in NFWR. The less secure larval habitat within the LR makes larvae more susceptible to capture, and coupled with reduced crayfish populations, translates to fewer adult C. alleganiensis. Larvae were more efficiently collected by skin-diving than wading and turning rocks in these habitats. With the exception of the LR population, which is composed of 48% gilled or gilled sized larvae, all recorded populations are almost entirely composed of adult and sub-adult age groups and small larvae, especially gilled larvae are either uncommon or unknown.