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Abstract: For conservation and planning practice, existing data – databases, maps, aerial photos, and researches – can be maximally used in GIS-based applications. Our primary goal was to compose the maps of the actual vegetation site types in 16 key areas, which are significant for conservation purposes in Saare County, covering a total area of 111 km2 (3.82% of Saare County). The main goal of this project was to develop a methodology for vegetation mapping in conservation areas and potential NATURA 2000 areas. The base data included the classification of Estonian mesoscale landscape units, the vector map at a scale of 1:50 000, the CORINE Land Cover vector map at a scale of 1:100 000, the cadastral map (raster-format land use type map) at a scale of 1:10 000, prints from CIR aerial photos (1:10 000), and printed maps of the soil types (1:20 000). The classification of Estonian vegetation site types was used to interpret the vegetation map. The Estonian biotope list was used to integrate field studies, aerial photos and maps. Route mapping was performed using CIR aerial photos and cadastral maps. All maps were integrated and analysed using MapInfo software. A map of mesoscale landscape units subtypes displays the vegetation site types, which are characteristic to each specific unit. In order to present a representative occurrence of the range of vegetation site types, 10% of subtype area needs to be mapped. Our work showed that best results were gained using land use maps, CIR aerial photos and soil maps in combination with field investigations. [Copyright &y& Elsevier]