Small demographic size and reduced genetic diversity increase the extinction probability of a population. Genetic diversity within populations for neutral markers is an heuristic parameter, as it reflects past and ongoing processes acting on populations, and informs on possible futures. This study presents a synthesis of the knowledge on neutral genetic diversity for threatened plants in metropolitan France and the use of such data in management actions. Pairing threatened species with the closest non-threatened species for which we could find appropriate genetic data, we collected information on genetic diversity for 25 threatened species and non-threatened controls. We found that threatened species in France have on average a lower within-population genetic diversity than non-threatened controls and thus are exposed to risks linked to genetic erosion. Combining an analysis of recovery plans and a survey addressed to practitioners, we concluded that genetic diversity is rarely integrated in management actions. The integration of such information into applied conservation remains a challenge. We provide some guidelines to collect biological traits impacting within-population genetic diversity and some specific recommendations for a better incorporation of population genetics concepts into conservations actions.