We conducted a habitat suitability assessment for two burrowing rodents, Anatolian or Nehring's blind mole rat (Nannospalax xanthodon) and Harting's vole (Microtus hartingi), on the island of Lesvos using a niche-based approach. We collected data on the presence of the two species across the island and selected several environmental variables, including land cover, geology, and habitat topography, to assess their influence on habitat suitability. We used the Maxent species distribution modelling algorithm to predict suitable habitats. The results showed that both species preferred habitats with low slopes and specific geological substrates, i.e., alluvial deposits and volcanic rocks. M. hartingi showed a preference for open habitats such as saltmarshes and non-irrigated arable land, while N. xanthodon preferred non-irrigated arable land, pastures, and discontinuous urban fabric. The model predicted a wider area of suitable habitats for Microtus hartingi compared to N. xanthodon. Interestingly, the two species are absent from the southeastern part of the island despite our model predicting high suitability; this indicates that a natural barrier of hilly terrain, extensive pine forests, and limestone rock formations may exist that impedes dispersal. Our study provides valuable insights into the habitat preferences of these two burrowing rodents on the island of Lesvos, which can inform biodiversity conservation and ecosystem management strategies.