None of the four major theoretical frameworks dealing with metropolitan governance – metropolitan government, public choice, new regionalism and reterritorialization – can explain the governance mechanisms of a cross-border agglomeration. Thus, we aim to use the transboundary agglomerations of Basel and Geneva as an empirical laboratory to fill this gap. The Basel metropolitan region covers three different countries, but Geneva has more public entities in its metropolitan governing body. This will allow us to distinguish the effect of the transnational variable from the effect of institutional fragmentation. To avoid conducting an apolitical analysis that refer to global market forces as the primary factors shaping metropolitan governance (eg. Sassen 1991), we will combine the urban regime framework (Stone 1989) that analyses power relationships between public and private actors with the Rescaled Competition State Regimes of Brenner (2004) who considers that metropolitan areas are primarily structured by socio-economic flows. Our empirical analysis will focus on two policy domains: transport and agriculture. Public transport has always been a priority since the introduction of the federal policy for agglomerations in 2001, whereas agriculture was first omitted, and then slowly integrated. Our two cases also differ in relation to these policies. Transboundary public transport remains more developed in Basel despite the recent opening of the Léman Express in Geneva. On the opposite, cross-border agriculture barely exists in Basel but dates back to the 19th century in Geneva, thanks to free-trade zones on the French territory.