1. The effect of habitat fragmentation on freshwater species has been addressed using brown trout Salmo trutta L. as a model species with a dendritic population structure.
2. Microsatellite loci were employed as molecular markers. Levels of gene flow and population subdivision were determined in more than 1200 brown trout individuals inhabiting four south European rivers with contrasting patterns of fragmentation, defined by the presence of barriers.
3. The genetic units in the four rivers were restricted by artificial barriers, and gene flow among samples within each river was associated with the level of fragmentation of the river.
4. Loss of genetic diversity and dislocation of the dendritic model have been detected in fragmented rivers. These results emphasise the importance of mitigating the impact of dams by constructing passages to restore gene flow along the river, for fish and other migratory species, as well as the need for caution in relation to stocking in isolated areas to avoid problems of inbreeding.