The Persian Squirrel (Sciurus anomalus) is a Southwest Asian species of squirrel with a single European Union population on the island of Lesvos in Greece. We evaluated the impact of land cover and tree density habitat variables on squirrel spatial distribution on the island. Our analysis was based on 240 localities of recorded occurrence of the species across the island, as well as 240 pseudo-absence localities, with land cover and tree density habitat variables at each locality. A total of 31 variables were analysed by principal component analysis (PCA). The significant predictors obtained from PCA were then used to obtain a binary logistic regression model to represent relative likelihood of occurrence and habitat suitability for this population. Lesvos Persian Squirrels appear to use all main arboreal vegetation types on the island, including both woodland as well as tree crops, especially olive cultivation. They are also found in rather small and isolated patches of such vegetation. However, although pine trees provide cones as a regular food source, the species is remarkably absent from larger areas of continuous coniferous forest and pine trees appear to be used only when mixed with or close to broad-leaved trees. Even though the Persian Squirrel is quite widespread on Lesvos, this population may still be at risk from habitat changes due to changing agricultural practices or urban expansion.