Organic Agriculture methods have a great potential in the field of nature conservation, both at the farm agroecosystem level and at the regional territorial level. Policy decision-makers need accounting and evaluation tools able to assess this potential in order to provide for suitable agri-environmental policy measures. By means of this study case we intend to propose a new Environmental Accounting methodology that has been developed at farm level to measure the environmental externalities (goods and services) generated by farm productive cycles. Methodology comprises both data collecting tools on farm environmental capital and tools for the monetary evaluation of environmental externalities. During this stage of “Environmental Accounting in Agriculture” research project we have constructed an Environmental Accounting Questionnaire. Questionnaire has been tested in two farms located in two different Tuscany Natural Park. Data on agroecosystems biodiversity were collected together with data on environmental quantities more directly involved in farm management and on the conservation of Water and Soil environmental systems abiotic resources. Environmental Accounting Questionnaire is organized in modules. Farm agroecosystem is divided in several environmental systems and subsystems. At each subsystem corresponds a module. Subsystems analyzed were chosen in function of environmental critical points observed in Tuscany geographic areas. Processing of data collected during first stage of the research project is presented. In this phase we have particularly focused on the analysis of vascular plants biodiversity observed in farms under survey.