While the emergent field of conservation genomics gains in popularity, empirical examples using such approaches in applied conservation practices are still lacking for many species of high conservation concern. The European sturgeon was the most widespread sturgeon species all over Europe, but its abundance has been drastically reduced to be now on the brink of extinction. Only a single population is surviving in the Gironde-Garonne-Dordogne watersheds (France) where the last known natural spawning occurred in 1994. In the years that followed, a sturgeon restoration program has been launched to build up a broodstock and repopulate this watershed. Our recent work using a set of microsatellites markers has characterized genetically the relict population, analyzing individuals of wild origin, captive-wild breeders, and seven generations issued from the breeding program, captured in the Gironde Estuary. Here, we will present main conclusions of this study concerning the levels of genetic variability and structure, effective population size, relatedness and inbreeding within the captive broodstock and the stocked population, with a special emphasis on several limitations of these data for the monitoring of the species in the future. While we are currently developing specific SNPs markers, we will discuss the putative pertinent contribution of such genomic data for the management and conservation programs of this threatened species, such as to gain more powerful kinship assessment, to improve inbreeding and demographic estimates and to explore genetic variation associated with fitness or adaptation