This paper describes an integrated GIS-based methodology for conservation value assessment using the traditional species-based and a habitat-based multi-criteria evaluation. The methodology was applied to 49 small islands and islets in the East Aegean area, belonging to a SCI Natura 2000 site. The species-based (botanical approach) conservation status assessment attributes a specific weight to the parameter of endemism, while the multi-criteria evaluation (MCE) approach emphasises the criteria of diversity, rarity, naturalness, replaceability and threat on each habitat type in combination with the number of significant taxa. The conservation values attained from the two approaches are significantly correlated, but the multi-criteria approach is more effective as it includes all the habitat types within the study area in the 25% of the polygons with the highest conservation values. Furthermore, results from the multi-criteria analysis were more in line with subjective assessments of the conservation value of the habitat types than the ones obtained by the botanical approach.