Gudgeons represent small, morphologically highly variable cyprinid fish. As a consequence, their systematics and taxonomy has been subject of numerous revisions. With the increased use of molecular data new light is shed on species subdivision, taxonomy, geographic distribution and patterns of interspecific and intergeneric hybridization. Recent studies on systematics, phylogeny and phylogeography of gudgeons mainly focused on eastern and southeastern European species. Here, I focus on gudgeons from the Austrian Danube system, as it is not yet clear which species actually inhabit the Austrian Danube system. Therefore I generated sequences from 139 specimen of the genera Gobio and Romanogobio of one nuclear (RPS7) and two mitochondrial (COI, D-LOOP) genes and analyzed them together with previously published data on gudgeons from all over Europe. Phylogenetic inference as well as haplotype network construction suggest that the Austrian Danube system is inhabited by a Gobio hybrid swarm. This hybrid swarm comprises three divergent mitochondrial lineages that cluster with western, eastern and southeastern Gobio species, respectively. Genetic distances among these mitochondrial lineages suggest that these lineages diverged about one million years ago, thus predating the last few glacial cycles of the Pleistocene. Little intra-lineage divergence imply recent, probably postglacial recolonization and admixture of these lineages in the Austrian Danube system is observed. In contrast, the four Romanogobio species native to Austria (including a new species presumably endemic to the upper Mur River) appear more clearly defined both in terms of morphology and genetics, despite signatures of occasional past and/or ongoing intergeneric and interspecific hybridization.