We investigated the origins of the fallow deer (Dama dama dama) of Rhodes by both morphological and molecular means. Our results show that these deer have homogeneous phenotypic patterns. All specimens fell within the common colour coat variety typical of the wild form. The Rhodian deer appear to be rather small, especially when compared with specimens from central and northern Europe. We then sequenced the HVR-I of 13 deer from Rhodes and compared these sequences with other 31 samples obtained from different European and Anatolian populations of fallow deer. Out of 44 sequences, 23 haploypes were found. When compared to the Turkish and Italian populations, the population of Rhodes revealed lower values of within population genetic diversity. The fallow deer from Rhodes are characterized by an 80-bp mitochondrial DNA (mtDNA) insertion not found elsewhere. As a consequence, all the deer from Rhodes form a tight cluster, distinct from all other fallow deer populations. This uniqueness makes the conservation and management of the Rhodian population particularly urgent.