The EU Biodiversity strategy 2020 directs Member states to map and evaluate the state of ecosystems and ecosystem services at their area by the 2014. At the same time, an economic value of these services should be assessed. In connection with this strategy we have created a methodology that aims to provide a unified conceptual framework and main rules for an assessment of ecosystem services in the Czech republic. The main objective is to set basic rules and procedures for an assessment and mapping of the state of ecosystem services, especially in respect to the forthcoming national assessment. The methodological framework serves to the Ministry of environment as a basis for design of policies and strategies in the field of biodiversity protection.