Most current methods to assess connectivity begin with landscape resistance maps. The prevailing resistance models are commonly based on expert opinion and, more recently, on a direct transformation of habitat suitability. However, habitat associations are not necessarily accurate indicators of dispersal, and thus may fail as a surrogate of resistance to movement. Genetic data can provide valuable insights in this respect.We aim at directly comparing the utility of habitat suitability models for estimating landscape resistance versus other approaches based on actual connectivity data.We develop a framework to compare landscape resistance models based on (1) a genetic-based multi model optimization and (2) a direct conversion of habitat suitability into landscape resistance. We applied this framework to the endangered brown bear in the Cantabrian Range (NW Spain).We found that the genetic-based optimization produced a resistance model that was more related to species movement than were models produced by direct conversion of habitat suitability. Certain land cover types and transport infrastructures were restrictive factors for species occurrence, but did not appear to impede the brown bear movements that determined observed genetic structure.In this study case, habitat suitability is not synonymous with permeability for dispersal, and does not seem to provide the best way to estimate actual landscape resistance. We highlight the general utility of this comparative approach to provide a comprehensive and practical assessment of factors involved in species movements, with the final aim of improving the initiatives to enhance landscape connectivity in conservation planning.