The Lusitanian pine vole ( Microtus lusitanicus (Gerbe, 1879)) and the Mediterranean pine vole ( Microtus duodecimcostatus de Selys-Longchamps, 1839) are sister species with burrowing habits and a restricted European distribution. Our aim was to assess the relative effect of environmental, soil, and spatial characteristics on the distribution of these species in Portugal, and obtain predicted occurrence maps for each species, particularly to identify areas of sympatry. We used spatial eigenvector mapping (SEVM) to describe the spatial autocorrelation in species data, and we partitioned the variance in species distributions to quantify the relative effects of environmental, soil, and spatial characteristics. The spatial variables explained the major part of variability in both species distributions and were more important than environmental or soil variables. The Lusitanian pine vole occurs in areas outside landscape units of grassland, higher rainfall, frost, and cambisols, with mostly acid soils, lower abundance of litosols, and presence of solonshaks. The Mediterranean pine vole is distributed in grassland areas within intermediate values of soil pH, dominated by litosols and luvisols, and lower rainfall, frost, and cambisols. Our results showed disjunct sympatric areas of small size and a parapatry boundary for the centre of Portugal, suggesting that contact zones are probably narrow.