Despite considerable efforts and funding, the reform implementation process in the Republic of Moldova meets important difficulties especially in the areas of strategic significance including the fields of public administration, justice and banking sectors. The initiatives implemented in these sectors by the Moldovan authorities under European supervision proved to be inefficient as they did not reach the expected results. This situation leads to dragging down the pace of European integration of the country, as the trust of the population and of foreign partners regarding European future of Moldova was negatively affected. Thus, this research intends to identify the most important impediments of bi-lateral cooperation between the Republic of Moldova and the European Union. Also, some recommendations are provided to increase the actual status-quo and are specified main Moldovan economic advantages which have been registered since the acceleration of cooperation with the EU.