One of the conservation projects carried out by the Ordesa y Monte Perdido National Park is the monitoring of the protected Spanish Moon Moth, Graellsia isabellae (Saturniidae), in several sites within the actual park, buffer zone, and peripheral area. Here we studied the genetic diversity, geographical structure, and connectivity of this iconic insect in those areas with the aim of producing evidence-based recommendations that might help the National Park staff in their decision-making. For this, we non-lethally sampled 402 adult moths from 17 sites and worked at two geographic scales: Western/Central Pyrenees and the area monitored by the staff of the National Park. The multilocus genotypes obtained for nine nuclear microsatellite markers allowed us to quantify genetic variation, investigate population structure, and calculate recent migration rates. Our results revealed a large-scale (ca. 125 km) west–east cline in allele frequencies that causes low overall genetic differentiation (FST = 0.038) and similar levels of diversity among sites. Habitat connectivity revealed as an important element determining dispersal for G. isabellae, given the patchy distribution of the host plant (Pinus sylvestris) in the study area. Gene flow within and outside the National Park was proved, with a particular site of the buffer zone (Bujaruelo) acting as a source of migrants to other localities within and outside the National Park. This finding underlines the importance of considering buffer zones to preserve genetic diversity within protected areas, and that safeguarding the connectedness of pine patches is key to the conservation of this iconic moth.