Gobiiformes are one of the most versatile groups among teleosts and show countless adaptations. Their fossil record encompasses numerous otolith-based species, but only a few species that are based on skeletons, and fossil skeletons with otoliths preserved in situ are exceptionally rare. Here, articulated skeletons, some with otoliths in situ, from the lower and middle Miocene of Southern Germany (Illerkirchberg, Öhningen) are re-investigated to clarify whether “Cottus brevis Ag.” and “Cottus brevis Ag.?” correspond to the same species. Our data show that the latter actually represents a previously unrecognized new species, for which we introduce the species epithet gaudanti. In both species, the palatine is T-shaped and the entopterygoid is absent, as is characteristic for the Gobiidae, but the number of branchiostegals is six, which is typical for the sleeper gobies (Eleotrididae and Butidae). This character combination is so far unique and justifies the introduction of Eleogobius, new genus, including E. brevis (Ag.) (as type species) and the new species E. gaudanti. A further outcome is that all otoliths previously described as Gobius multipinnatus (H. v. Meyer) rather belong to E. gaudanti, new species, and that the otoliths of G. multipinnatus remain unknown until a skeleton with otoliths in situ is found. Our results indicate that fossil Gobiiformes may have been much more diverse than the currently known record suggests, and that many fossil species of “Gobius” might not belong to this genus, or indeed even to the Gobiidae.