How frequently genes pass through a hybrid zone may be influenced by the environment. Accordingly, in long hybrid zones that span more than one environmental setting, different patterns may emerge. We reconstruct the amount and direction of gene flow across such a heterogeneous hybrid zone in two species of marbled newts (Triturus marmoratus and T. pygmaeus), in four widely separated areas of the Iberian Peninsula from one mitochondrial and three nuclear genes. The main environmental conditions associated with the position of the contact zone are determined as precipitation, rivers, altitude and relief. Elsewhere its position is not correlated with any environmental factor and is instead determined by the shortest geographical distance between fixed positions at either side (mountains in the East and river in the West). In areas where the position of the zone is stable, gene flow was bidirectional. Where T. pygmaeus has superseded Triturus marmoratus over a large area gene flow was unidirectional. The prediction that a major river would reduce gene flow was not confirmed.