The contribution of Green Infrastructure (GI) in vital areas such as regional development, climate change, agriculture, forestry and environmental protection is already acknowledged and listed as one of the priorities in several key EU policies, and is the basis for the EU Green Infrastructure Strategy. However, the concept is not yet fully integrated into actual planning strategies, in this respect the Czech Republic is no different. A major problem in doing so is a lack of guidelines/ how to identify and map GI using available sources and thus keeping costs down. The existing data sources for land cover or land use often do not fulfil the requirements in terms of thematic coverage, resolution or accuracy. In order to work around such limitations, we analyse the existing land use/land cover data in the Czech Republic from the GI perspective. Furthermore, we propose a GI mapping methodology based on the diagnosis of three mapping approaches at the regional level, grounded on the utilisation and processing of different data sets. We compared GI maps based on European data from CORINE Land Cover Database, Czech national database called Consolidated Layer of Ecosystems (CLE) and combination of Czech national and regional data and manual vectorization. Our results show that CORINE based GI map is suitable for transnational scale but unsuitable for regional scale. The CLE based GI map is good for both national and regional scale but its information on GI in urban areas is lacking. The detailed regional GI map is good for regional and to some degree even for local scale but its creation is time consuming. However, careful combination of existing national and regional data can provide good outcome in creating GI map usable for territorial planning.