The file contains microsatellite data (21 loci) from six wild brown trout populations in Western Jutland, Denmark, along with samples from two hatchery strains used for stocking the rivers. The samples from the wild populations consist of contemporary samples (2000-2006) and historical pre-stocking samples (1927-1956), the latter obtained by analyzing DNA from archived scale samples. See Hansen et al. (2009) for further details on the data and study. The file format is MSA [Dieringer D, Schlotterer C (2003) Microsatellite Analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167β169]