The stellate sturgeons as well as the other sturgeon populations inhabiting the Lower Danube River system (LDR) and the NW part of the Black Sea have experienced a severe decline due to heavy fishery, river regulation and water pollution. Traditionally, sturgeons have represented a great economic value for the countries along the Danube, being fished mainly for their eggs, the “black caviar”. The human population along the Danube River took advantage of the anadromous behaviour of these fishes and over decades of overfishing they depleted the stocks. In 2006 the Romanian government banned the commercial fishing of sturgeons for a period of 10 years and started a Supportive Stocking Programme of Danube with farmed juveniles originating from wild parents. The present study focuses on whether there are genetically isolated subpopulations among the adult cohorts of stellate sturgeons migrating into the LDR in the year 2010, and whether the genetic characteristics of YOY samples in the same year supports the existence of such subpopulations. Samples from fall and spring migrants and from YOY stellate sturgeons naturally born in the river in 2010 were genetically analyzed for mtDNA cyt b and D-loop regions as well as a panel of nuclear microsatellites, and revealed considerable individual variability. Hardy-Weinberg conformity tests revealed heterozygote deficit at 3 out of 4 microsatellite loci. Based on the genic differentiation at the microsatellite loci and mtDNA and cluster analyses, a genetically distinct group were demonstrated among the 2010 YOY samples, pointing to the existence of a previously unknown population substructure within the stellate sturgeons of The Lower Danube River. This was supported by biological characteristics of the YOY samples.