In this paper we develop a framework of analysis for the main economic issues that arise in the pursuit of system of labelling for GM and non-GM products under the introduction of GM products. This model represents a vertical relationship with three stages in the supply chain: manufacturer, retailer and final consumers. Co-mingling may occur between non-GM and GM products: contaminated non-GM products may be sold on the final market. To avoid this, the retailer induces his supplier to make tests before the sale. The retailer accepts lots if the GM content is under the public labelling threshold. Above the threshold, lots are sold by the manufacturer on a GM market. Public regulation takes the form of the purity threshold or labelling threshold. The impact of the firm’s strategies takes the form of the effort (segregation measures) and the sampling size set up by the supplier/manufacturer. Strategic games analysis is used to evaluate impacts of private and public policies on stakeholders’ trade-offs and on the GM/non-GM coexistence. The model can highlight the opposite interests between the stakeholders regarding the labelling threshold s, the level of effort e and the purity of the raw material. The retailer and the consumers prefer average labelling threshold, average effort and average non-contamination rate of raw material while the manufacturer prefers a slackened labelling threshold and small segregation effort.