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The analysis of fragmentation and habitat connectivity is important in determining their conservation status and ensuring their long-term survival. However, the reliability of assessments on habitat conservation status may depend on the resolution of forest cover maps used as inputs. The aim of this paper is to quantify differences in the results of habitat fragmentation and connectivity analysis found when using three different forest cover maps of various resolutions, and discusses their effect in the assessment of habitat conservation status. The study was conducted in a Natura 2000 habitat (9120:Atlantic acidophilous beech forests) in Spain. To measure fragmentation, we carried out a morphological spatial pattern analysis (MSPA) which provided a very detailed spatial landscape description (core, islet, bridge, loop, branch and perforation elements).