One of the major problems in the anguilliform Clariidae is the taxonomical validity and the systematic position of Gymnallabes nops. This vagueness is largely due to the fact that the description of this species is based on the holotype only, and no additional specimens are known. This also means that past studies on this holotype were limited to non-invasive research, such as external morphology and X-rays. These methods, however, yield only a limited number of valuable characters. In this study a high-resolution desktop X-ray microtomography instrument (CT-scan) was used. This enables us to confirm the results of the radiographies but also to perform a detailed osteological study, without damaging the holotype. The osteological survey showed similarities with other anguilliform clariids, in particular with Platyallabes tihoni and Gymnallabes typus. Besides these traits, G. nops shows a set of characters, revealed in this study, unique among the clariids, such as a reduction of the infraorbital bones in number and size, a large anterior outgrowth of the opercle, a clearly visible epiphyseal bridge and the typical positioning of entopterygoid and metapterygoid bones. These extra results may help to clarify the validity and the phylogenetic position of G. nops.