Most natural populations of Eurasian sturgeons have declined dramatically during recent decades, reaching historic low levels today. During the same period, sturgeon has become very popular in European aquaculture. Because many hatcheries are located near rivers, their unintentional escape is often documented, especially during floods. Until now, no cases of successful hybridization of these escaped fish with wild stocks have been reported. In this study, the genetic structure of a highly threatened population of sterlets (Acipenser ruthenus) from the Upper Danube was analysed as a requirement for their conservation. Surprisingly, we observed genotypes and morphotypes of Siberian sturgeon (Acipenser baerii), as well as hybrids between this species and native sterlets. This hybridization poses a serious threat for the survival of this isolated sterlet population in the upper part of the Danube. For the first time, natural reproduction is documented for Siberian sturgeon outside their natural range in Europe. This finding demonstrates the risk of extinction by hybridisation of endangered populations. We would like to stress that taking into consideration the risks for native sturgeon populations, farmed sturgeon should not be released into the wild, and all measures should be taken to prevent their accidental escape.