Genetic diversity was analysed in Salmo trutta populations living in an area of central Italy by sequencing 310 bp of the 5′ end of the mtDNA control region (D‐loop) and by Restriction Fragment Length Polymorphism (RFLP) analysis of three mtDNA segments. Data show a genetic structure profoundly altered by stockings with allochthonous material of Atlantic origin. In fact, 15 of the RFLP haplotypes detected are linked to an Atlantic sequence. The remaining 9 were instead coupled with sequences representing the three major phylogenetic lineages previously identified in the Mediterranean basin (Adriatic, marmoratus, and Mediterranean), representing the native genetic diversity of brown trout in that area. The close genetic affinity observed between these latter haplotypes and those found in the Balkan peninsula by other authors seems to be in accordance with a recent, natural, history of dispersion between the two borders of the Adriatic Sea. These results appear significant from a conservation point of view as, in spite of the massive stocking with hatchery‐reared specimens, they highlight the persistence of Salmo trutta native genetic diversity in central Italy.

The genetic variability of the wall lizard, Podarcis muralis, was analysed in that part of its range regarded as its area of origin and also its expansion centre. The analysis was performed on partial cytochrome b sequences (405 bp) of 117 specimens representing 31 sampling locations from southern, central and northern Italy. The results of this study revealed 30 haplotypes in the Italian sample belonging to three main genetic lineages. The genetic divergence among haplotypes ranged from 0.2 to 6.6%, whereas the estimation of divergence times among mtDNA lineages highlighted a complex pattern of genetic differentiation with both Pleistocene and Pliocene divergences (3.2–0.7 Ma). These results put in evidence the role played by the pre-Pleistocene and Pleistocene palaeogeographic and palaeoclimatic events in shaping the genetic diversity of the wall lizard in Italy and confirm the role of this peninsula as glacial refuge. In addition, AMOVA analysis revealed the presence of geographically structured clades indicating the occurrence of multiple glacial refugia in Italy, thus supporting a refugia-within-refugia scenario for the wall lizard in Italy. Finally, the results of this study seem to indicate a lack of congruence between the four morphological subspecies currently recognised in the Italian Peninsula and the main genetic lineages detected.