Identity preservation (IP) refers to a system of production, handling and marketing practices that maintains the integrity of and purity of agricultural commodities. Products segregation plays a key role in IP, but an IP system is more demanding, namely due to testing requirements. Labelling regulation for GM containing or derived food and feed in EU, as well as some food manufacturers’ prerequisite of GM-free raw materials, prompted new developments of IP systems that are now part of the modus operandi of major supply chains. A research on the Portuguese maize bread supply chain, a minor maize supply chain in value but large due to the myriad of actors it involves, was conducted in order to understand if and how GM labelling regulation is accomplished. Direct interviews to several stakeholders along the maize bread supply chain evidenced a large heterogeneity in awareness and performance of GM-labeling rules. But results also reflected heterogeneity in awareness and performance regarding other traits, including traits envisaged by Codex Standards or traits associated to traditional maize bread, as it is the case of flint type varieties and, moreover, the IP of maize landraces, traditionally grown for bread making and that are still grown by some farmers. Altogether these results encouraged a comprehensive discussion of implementation of IP systems and suggest that isolating non-GM maize IP and its costs from the comprehensive IP system of each supply chain might be misleading.