Abstract The high diversity of extant gobiids (Gobiidae: Teleostei) makes taxonomic and phylogenetic interpretation of fossil members of the clade a difficult task. To facilitate future taxonomic and systematic work on the group, we have assembled a morphological reference database encompassing skeletal characters, an otolith atlas and otolith morphometric data of 25 present-day species from the European Gobius lineage (s.l.) that represent 18 different genera and include all nine sublineages. We show that: (1) skeletal traits and morphometric otolith variables can be diagnostic for a sublineage; (2) otolith morphology allows identification at the genus and species levels; and (3) the number of anal-fin rays and details of the otolith margins can be used to discriminate closely related dwarf gobies. The skeletal and otolith characters are largely stable in the marine gobies analysed here, whereas freshwater gobies (Padogobius, Ponto-Caspian gobies) are far more variable. This might be related to the conquest by Padogobius and Ponto-Caspian gobies of freshwater and low-salinity habitats, in which environmental conditions can fluctuate widely. We anticipate that the database presented here can be used as a valuable reference tool to assess the relationships of fossil gobiids and increase our knowledge of the evolutionary history of the group as a whole.