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The socio-ecological system dominated by pastureland in the Asteroussia Mountains (Crete, Greece) was analyzed over a long time interval (1945–2010) to identify the most relevant system’s characteristics and changes. Vegetation cover and land-uses have been quantified by analyzing aerial photographs exploring the whole study period. Soil characteristics have been assessed by carrying out an extensive field survey for the last reference year (2010) and by estimating the average soil loss for the past period using the PESERA soil erosion model validated by field measurements. Based on environmental, social and economic attributes, three major periods characterizing the socio-ecological system of Asteroussia Mountains have been distinguished. During the first and second period, the land was satisfactorily managed with moderate–low soil erosion rates despite the adverse (prevailing) soil, topographic and climate conditions for vegetation growth. The third time interval featured a rapid growth in the livestock density causing increased soil erosion rates, loss in plant productivity, and a generalized over-exploitation of natural resources. As a consequence, the desertification process has significantly increased in the last period. The analysis of the long-term evolution of socio-ecological system provided evidence to understand the main drivers of land degradation and to recommend mitigation policies specifically addressing Mediterranean pastureland.