The modern Gobioidei (Teleostei) comprise eight families, but the extinct †Pirskeniidae from the lower Oligocene of the Czech Republic indicate that further families may have existed in the past. However, the validity of the †Pirskeniidae has been questioned and its single genus †Pirskenius has been assigned to the extant family Eleotridae in previous works. The objective of this study is to clarify the status of the †Pirskeniidae. Whether or not the †Pirskeniidae should be synonymised with the Eleotridae is also interesting from a biogeographical point of view as Eleotridae is not present in Europe or the Mediterranean Sea today. We present new specimens and re-examine the material on which the two known species of †Pirskenius are based (†P. diatomaceus Obrhelová, 1961; †P. radoni Přikryl, 2014). To provide a context for phylogenetically informative characters related to the palatine and the branchiostegal rays, three early-branching gobioids (Rhyacichthys, Protogobius, Perccottus), an eleotrid (Eleotris) and a gobiid (Gobius) were subjected to micro-CT analysis. The new data justify revalidation of the family †Pirskeniidae, and a revised diagnosis is presented for both †Pirskenius and †Pirskeniidae. Moreover, we provide for the first time an attempt to relate a fossil gobioid to extant taxa based on phylogenetic analysis. The results indicate a sister-group relationship of †Pirskeniidae to the Thalasseleotrididae + Gobiidae + Oxudercidae clade. Considering the fossil record, the arrival of gobioids in freshwater habitats in the early Oligocene apparently had generated new lineages that finally were not successful and became extinct shortly after they had diverged. There is currently no evidence that the Eleotridae was present in the European ichthyofauna in the past.