Genetic variability is the only chance for species to evolve and adapt to environmental changes. Since the beginning of this century, conservation genetics has investigated the origin of genetic diversity and tried to correlate natural events, historical processes, and human influence with the distribution of species, genes, and alleles. Deer are very common in both the Old and New Worlds, although some species have expanded and evolved, while others have been drastically reduced or even gone extinct. Over the past 20 years, conservation genetics’ biomolecular approach allowed researchers to deepen the understanding of the evolution of these species. Through the study of genes and genomes, it was possible to recognise and describe the gene flow among populations, the hybridisation events between species, and the natural or anthropogenic barriers that have created and moulded the distribution of genetic diversity currently described in deer. The contribution given by conservation genetics permitted researchers to understand which factors mainly caused the reduction of genetic variability in those species that were threatened and then extinct, but also to furnish the right advice to counteract the reduction of variability in other species that are critically endangered but yet viable. Again, conservation genetics allowed researchers to define the existence of evolutionary significant units (ESUs) and evolutionary management units (EMUs) and thus to promote the establishment of management plans for their protection; similarly, it demonstrated how the releasing or restocking of allochthonous individuals has contributed to the loss of autochthonous genetic pools. The knowledge provided by conservation genetics has been recently complemented by data from conservation genomics, which focuses on gene annotation and genome-wide association studies (GWAS) to provide novel correlations between habitat and species adaptation.