The Mediterranean island of Sardinia is known for its multitude of unique genetic lineages. We view one of them in a larger phylogeographic context. The endemic Sardinian Meadow Brown butterfly, Maniola nurag, is restricted to the mountainous areas of the island, whereas its widespread close relative, Maniola jurtina, also occurs on the coast. At intermediate altitudes the species’ distributions overlap. There, a number of individuals exhibit phenotypic characteristics intermediate between the two species. We examined patterns of intra- and interpopulation variation in 10 M. nurag populations from Sardinia and 16 M. jurtina populations from Sardinia and continental Europe, as well as 17 intermediate individuals, sampled in 1999–2002, by means of allozyme markers, combining it with a morphometric analysis based on 18 wing-characters of 52 males. At the 15 loci studied (aldolase, aat-1, aat-2, g6pdh, gpd, idh-1, idh-2, mdh-1, mdh-2, mpi, me, leu-ala, pgi, pgm, and 6pgdh), 76 different alleles were detected, 63 of which were shared by M. nurag and M. jurtina. None of the loci was found to be alternatively fixed between the two species. In that respect, this study testifies to the difficulties that may arise when trying to identify hybrids from genotypic data. Levels of genetic variation in island populations (M. jurtina: HO = 0.137–0.189; M. nurag: HO = 0.141–0.270) were comparable to those of mainland M. jurtina (HO = 0.141–0.236). A Bayesian admixture analysis supported the hypothesis of mixed (hybrid) ancestry of individuals occurring at intermediate altitudes. Similarly, neighbour-joining and unweighted pair-group method with arithmetic averaging (UPGMA) analyses, as well as morphometrics hinted at the existence of a Maniola-hybrid zone in Sardinia at intermediate altitudes. We discuss the results in the light of the phylogeography of other Sardinian taxa with the aim to reach a general understanding of the biogeographic history of this island's endemic species.