The study area is Šumava National Park (ŠNP), the largest of the four national parks located in the south-west of Czech Republic, on the border with Germany. Being a unique mosaic of natural and secondary habitats of exceptional natural value of European- wide significance, the ŠNP is established as a special regime of environmental protection with unique biological communities. The area is represented by the vast wooded areas, precious mountain spruce and protected mixed forests of various ages, peat bogs, meadows biotops. Altogether, they create a unique mosaic of biotopes, which encompass a variety of rare, endemic and endangered species. Geobotanically, the ŠNP belongs to the Bohemian Forest divided into two national parks, located in Czech Republic and Germany. The research aim was to analyse how the ecosystem landscapes located within the study area changed since 1991 until 2009 (18-year time span) using remote sensing data and GIS. The data include GIS layers and Landsat TM images with 18-years interval (1991 and 2009). Methodology included following major steps: 1) Data capture; 2) GIS project. 3) Geo-referencing; 4) Activating GDAL remote sensing plugins. 5) Preliminary data processing. 6) Generating con- tour layers; 7) Landsat TM Colour composition; 8) Defining Study Area; 9) False colour composites; 10) Image classification; 11) Spatial analysis. The GIS analysis is used to test the importance of the natural and human-induced land used changes for survival of the important floristic locations in several case studies. The outcomes are illustrated by two maps showing geographic distribution of land cover types within the study area in given time periods of 18-year time span. The results demonstrate visualization of the ecosystems in 1991 and 2009 showing dynamics of land cover types in the given time. The work demonstrated effective application of QGIS software combined with multi-source data (remote sensing and geoinformatics) for the purpose of environmental protection of precious areas of the Šumava National Park,