The dendritic nature of freshwater streams presents unique conservation concerns. Linear streams are prone to fragmentation that can reduce or completely prevent animal migration. Understanding the evolutionary consequences of habitat fragmentation is critical for predicting population response and ultimately the likelihood of population persistence. The goal of this project is to gain further understanding of the genetic and evolutionary consequences of stream fragmentation. The project will apply an evolutionary perspective to the consequences of stream fragmentation on wild brook trout populations in Massachusetts. We will provide novel links between ecology and evolution to help predict population persistence of brook trout in fragmented stream systems. Because brook trout are an indicator species for cold, unpolluted stream habitat, our work will help conserve and retain the ecosystem integrity of this critical habitat type. We will combine a long-term ecological study of brook trout with novel genetic methods. These genetic methods will allow us to understand evolutionary change caused by habitat fragmentation. This information will ultimately be useful for prioritizing conservation efforts in stream systems influenced by anthropogenic fragmentation.