The coexistence between genetically modified (GM) and non-GM based agricultural supply chains is an economic institution that defines rules of the games, the objectives of which are set more broadly than economic rationality and efficiency. Institution of coexistence covers the formal rules as well as informal constraints devoted principally to identity preservation and segregation, and the ways how they are imposed and enforced in the GM and non-GM based supply chains from agri-food sector. They applies to the dynamic process of formulation, selection and adaptation of behaviors and rules, which form the institutional orders in local, regional and international dimensions, under the circumstances of constant changes in the socio-economic systems. The paper is an attempt to describe the coexistence as an economic institution in the light of New Institutional Economics. Using the results of foresight technique it also examine how the Transatlantic Trade and Investment Partnership under negotiation between the European Union and the United States could re-define both legal regulations and market-based standards of coexistence. In the Delphi method panels participated stakeholders from both GM and non-GM based agri-food supply chains, who forecasted that the institution of coexistence will be re-defined by the rules that TTIP would set up.