Since the 1960s, territorial organization has been drastically transformed in Southeast Asia. Two processes have given an impulse to these changes. On the one hand, States are still active, pursuing their internal “conquest”, mainly in mountainous areas, in order to consolidate their territorial legitimacy. On the other hand, States are moving toward a better integration into supranational systems, driven by economic globalization. Far from having lost their “territoriality”, Southeast Asian States have succeeded in dipping into these systems, especially in those related to environmental matters, allowing their governments to increase their internal territorial control. The first part of the article establishes the links between colonial and modern States interventions in marginal areas, especially looking at those which concern political integration, administration, agricultural colonization as well as forest management. In the second part, a cartographic and diachronic portrait of protected area networks in continental Southeast Asia is followed by considerations regarding the main challenges posed by this evolution, especially relations between States and their respective ethnic minorities. The conclusion underline questions regarding the links between the State and its territory and how we can interpret these changes.