Atretochoana eiselti can be readily distinguished from other caecilians by its sealed internal nostrils and massive mouth.

It was originally described as a species of the genus Typhlonectes (Taylor, 1968) but was subsequently placed in its own genus by Nussbaum and Wilkinson (1996). 

Although it is more closely related to Potomotyphlus than to Typhlonectes (Wilkinson and Nussbaum, 1998), it is morphologically very different from both these genera of aquatic caecilians.