Conservation genetics pinpoint the use of biological materials collected without stressing wildlife and antlers seem to fit with this need. In the State Nature Reserve “Bosco della Mesola”, Northern Italy occurs the only native red deer population of peninsular Italy, recently recognized as a distinct subspecies (Cervus elaphus italicus) and characterized by peculiar morphology and phenotype. We tested the applicability of a simple and inexpensive biomolecular protocol to obtain information for the conservation of endangered deer with no stress for animals. DNA obtained by drilling both well preserved and highly degraded antlers was amplified with three types of molecular markers to get comprehensive information at individual, population and species level. Our results pointed out that only the seal yielded amplifiable DNA. The study attested that weathered antlers can be a suitable source of DNA not only in dry but also in Mediterranean climates, characterized by strong seasonal fluctuations. Antlers are an efficient and cost-effective non-invasive sampling for molecular genetic studies on rare or threatened species of cervids. We tested and provided easy to use and cheap laboratory protocols implementing all the previous knowledge.