Anadromous brown trout along the Norwegian Skagerrak coast are genetically differentiated among streams, and there are indications of further substructuring within some streams. Among presumably long-standing populations there is a pattern of increased genetic differentiation with distance, indicating an isolation-by-distance effect. For trout that inhabit streams that have recently been recolonized after the extinction of trout because of acidification, we find evidence for a mixed origin of the recolonizing trout. Both the high levels of gametic phase disequilibrium and the clear deviation from the general pattern of increased genetic differentiation with distance that are seen in recolonized streams, are consistent with recent population admixture, and confirm the loss of the original populations of these acid streams.