The cross-border metropolitan area of Geneva has recently experienced a traumatic election in the Swiss central district « Canton de Genève ». During the campaign, two populist parties have stigmatized both the daily commuters from France as a work force which catches up the jobs in the inner city and the French suburbs as a shelter for criminals. The two political parties using these arguments have won the fourth of the elected members of the parliament of the Canton. These events express the contradictions between the political process of governance and planning integration at the scale of the cross border agglomeration and the increasing claim of isolationism on a xenophobic base in the central district. A new fast public transportation network is perceived simultaneously as a tool for a sustainable development of the whole metropolitan area or as a tool for an increasing colonization and exploitation of the center from the foreign periphery. The context of economic crisis is definitely a key factor of explanation of the strengthening of populist xenophobia and isolationism, but we argue that part of the issue is structural and related to the specific morphology of the cross border agglomeration which includes a green and agricultural buffer zone between the Swiss central district and the French suburbs.