The paper aims at the assessment of the main effects of signing the Association Agreement on the Moldovan agricultural sector, while examining its reaction, if the Republic of Moldova would have opted for its integration in the Customs Union - Russian Federation, Belarus, and Kazakhstan. During the period 2010-2013, Republic of Moldova launched a number of trade policy development initiatives in order to ensure a more facilitating legal framework for the economic and trade relations with the key external partners. An agreement on the establishment of a free trade area in the CIS was signed in this period. Similarly, Republic of Moldova started negotiating the Association Agreement with the European Union, which was signed in June this year and has as component part the Deep and Comprehensive Free Trade Agreement (DCFTA). The paper reveals that the signing of the Association Agreement with the EU could serve as instrument to stimulate the agricultural sector, but the DCFTA establishment will present some challenges, which are to be properly addressed, in order to exclude their turning into risks.