The Adriatic Sea and Adriatic Sea drainage system (or Adriatic region) is characterized by high levels of species richness. This especially applies to endemic fishes, as exemplified by the sand gobies. However, the diversity of this group is probably still underestimated. Several keys for gobiid identification, notably of the Adriatic region, have been proposed on the basis of morphological characters, but difficulties persist in species identification. Molecular phylogenies support the monophyly of the sand gobies, but relationships between genera and species remain poorly resolved. In this work, the diversity and evolutionary history of the Adriatic sand gobies (Pomatoschistus and Knipowitschia) were investigated by applying phylogenetic reconstructions, species delimitation tests, and molecular dating based on mitochondrial cytochrome b and nuclear rhodopsin 1 genes. The concatenation of both genes allowed, for the first time, the creation of a highly resolved phylogeny at the interspecific level. The generic diversity within the sand gobies is probably considerably higher than formerly assumed. Our results highlight cryptic diversity and suggest that new species remain to be described within Knipowitschia and Pomatoschistus. Most of all, our results emphasized the urgent need of a taxonomic revision of the sand gobies. Several past events were at the origin of sand goby diversification in the Adriatic region. It seems that glacial periods promoted the intraspecific diversification of the endemic species, whereas interglacial periods promoted the (re)colonization of the Adriatic Sea by more widespread species.