The world around us is changing more and more heavily influenced by human activity. We transform the landscape around us and thereby change the conditions of existence of different species and their habitats. For example forests fragmentation is shifting which influences connectivity of forest patches and affects animals movement. Therefore, for efficient spatial management or development of effective conservation mechanisms it is important to have the right tools and workflows that allow for complex evaluation of fragmentation and connectivity at landscape and species level. In this project we exactly focused on new models and measures development which allow quantitatively describe fragmentation and connectivity. We work with forests and protected species; brown bear and European bison. At each step of the analysis we used geographic information technology, among others, spatial data such as elevation models or satellite land cover maps and various analytical modelling methods. We have shown that our workflows can be successfully used in practice, e.g. to identify new directions in environment conservation plans that include identification of biodiversity hotspots and prevention of biodiversity loss, location of reintroduction sites for endangered species or delimitation of ecological corridors.