We present high-resolution X-ray microtomography (microCT) to enhance the standard morphological description of a recently described centipede, Eupolybothrus liburnicus Akkari, Komerički, Weigand, Edgecombe and Stoev, 2017. The 3D images of the holotype and paratype specimens are considered here as cybertypes for the species-a universal and virtual representation of the type material. This 'avatar' of the holotype is the first published male centipede cybertype. The microtomographic data of both types revealed further characters of systematic value and allowed us to hypothesise on the function of some of the male secondary structures and the mating behaviour of the species. Additionally, we compared part of the female reproductive system of E. liburnicus to species from the same genus, including E. cavernicolus Stoev & Komerički 2013, its closest congener. The high-resolution 3D image data have been uploaded to an open repository (MorphoSource.org) to serve in any subsequent study on the species and genus, as we believe this would catalyse biosystematic research on this and other arthropod groups.