The paper aims to analyze the evolution of the agricultural systems in the Republic of Moldova and to assess the impact of the structural changes over the national economy. In order to achieve this, there were used the following research methods such as: analysis of the economic indicators, methods of comparative analysis, analysis of the public policies’ impact on the agri-food sector and rural area. Moldovan agriculture is based on three agricultural systems: conventional, of subsistence and ecologic, which do not provide the performance of the sector and competitiveness of the agricultural products on the internal and international markets. In comparison with the neighboring countries which have recorded greater rates of agricultural production growth since 2001, Moldova has recorded more modest results, showing a stagnation in agriculture. This situation is associated with the major risks related to the structural changes that may affect the rural area and the economy as a whole, such as: the sharp decrease of rural population in some localities, aging, inefficient use and depreciation of assets in rural areas, decrease of the usage level of the bio-climatic potential. Currently , the agricultural systems that are based on farm products diversification, reducing dependence on imported resources, ecological agriculture and the trend towards the high value added products are under discussion and development.