After facing a great decline all over Europe during the past centuries, starting from the second half of the XX century the roe deer (Capreolus capreolus) was reintroduced and strongly managed throughout its range, as other ungulate species. Overhunting and habitat change were the main factors threatening roe deer populations in Italy, where small remnant populations of putatively native roe deer survived in a few localities of eastern Alps and central-southern Italy. We investigated the genetic variation of a roe deer population inhabiting the northern Apennines in the province of Massa-Carrara (Tuscany, Italy), analysing both mitochondrial DNA control region and a total of 11 autosomal microsatellite loci, to identify possible sources and recolonisation patterns, as well as the local prevalence of native Capreolus capreolus italicus gene pool. Analyses revealed an admixed nature of roe deer in this area, merging both native and non-native lineages, with a dominance of italicus haplotypes in the matriline and a majority of non-native genetic component in the autosomal markers. The high similarity with roe deer from neighbouring areas suggests a natural population origin by immigration. Two scenarios may explain the observed pattern of genetic variation: a colonisation by a limited number of immigrants from a single admixed source (either north or south-east), or a two-step recolonisation, firstly from the south, where the italicus ancestry was prevalent, and then from the north, mostly by individuals carrying C. c. capreolus genes. This study shows the genetic consequences of translocations even in populations not directly targeted by human interventions and highlight how investigating genetic variation might be essential in species management.