The use of surrogate species in conservation planning has been applied with disappointing results on relatively large sets of species. It could still prove useful for optimizing conservation efforts when considering a small set of species with similar ecological requirements, however few field tests of this nature have been carried out. The aim of this research is to compare the response of three arboreal rodent species—the fat dormouse (Glis glis), the hazel dormouse (Muscardinus avellanarius) and the red squirrel (Sciurus vulgaris)—to habitat loss and fragmentation, with the aim of identifying priorities for conservation and evaluating possible optimization of conservation efforts under different scenarios: habitat restoration and selection of focal patches. We studied the distribution of the three species in a sample of patches in a highly fragmented landscape in central Italy, using a patch-landscape scale approach. The distribution was studied by using hair tubes, nestboxes and nocturnal surveys. The three species showed analogous responses to increasing isolation and decreasing size of habitat patches; what differed however, was the magnitude of responses. Our results show possible application of surrogacy within this restricted group of species, however several caveats arise depending on the conservation strategy and available funding. If habitat restoration is the objective, then the fat dormouse should be the target species for guiding size and isolation of patches. On the other hand, the magnitude of the differences and patch requirements for this species, question the feasibility of these conservation actions. If selection of focal patches for conservation is the objective then selecting the fat dormouse as a focal/umbrella species would overlook areas suitable for the other two species. Feasible optimisation of conservation efforts may be possible only between the red squirrel and the hazel dormouse.