The Mesola red deer Cervus elaphus in the Po delta are the only native red deer population on the Italian mainland and have been the focus of conservationists and wildlife biologists for some time. In our study, we present a genetic analysis of 25 Mesola red deer on the basis of 20 polymorphic microsatellite loci, aiming at estimating the population's genetic diversity and at providing information for a future genetic screening. In addition, we carried out a population viability analysis (PVA) with demographic and life-history data available from a long-term population survey, simulating different management scenarios. Genetic diversity was very low compared to the rest of Europe (observed and expected heterozygosity 0.50 and 0.61, respectively), and an overall excess of homozygosity was indicative of inbreeding. Calculations of the probability of identity and genotype mismatch frequencies suggested that between five and seven highly informative loci were sufficient to resolve individuals with reasonable certainty. The PVA yielded a generally poor outlook, but at the same time, it showed that management measures already taken significantly increased population viability. A sensitivity analysis revealed that inbreeding depression and possible catastrophes had a huge impact on the population's prospects. However, the establishment of two subpopulations and successful attempts at reducing the consequences of catastrophic events were able to significantly mitigate the harmful effects of both inbreeding and environmental stochasticity. These results, in particular the splitting of the population, may be of general interest to conservationists dealing with unique threatened populations.