The Taiwan orogen has formed as a result of the arc-continent collision between the Eurasian continental margin and the Luzon island arc over the last 5 million years and is the type example of an arc-continent collision. The tectonic processes at work beneath Taiwan are still debated, and the available data have been interpreted with both thin-skinned and thick-skinned models. In 2004, the Taiwan Integrated Geodynamical Research (TAIGER) project began a systematic investigation of the crustal and upper mantle structure beneath Taiwan. TAIGER magnetotelluric (MT) data from Central Taiwan favour a thick-skinned model for that region. The Taiwan orogen becomes younger to the south, so the earlier stages of collision were investigated with a 100-km-long MT profile in southern Taiwan. Data were recorded at 15 MT sites and tensor decomposition and two-dimensional inversion were applied to the MT data. The shallow electrical structure is in good agreement with surface geology. The deeper structure shows a major conductor in the mid-crust that can be explained by fluid content of 0.4 -1.4%. A similar feature was observed in Central Taiwan, but with a higher fluid content. The conductor in Southern Taiwan extends to lower crustal depths and is likely caused by fluids generated by metamorphic reactions in a thickened crust. Together the Central and Southern Taiwan MT profiles favor a model with thick skinned deformation.