Global change significantly alters life history of many animal and plant taxa. However, its evolutionary consequences are relatively less examined especially at large spatial scales. If environmental change modifies migration or dispersal patterns, the level of gene flow among populations would also be altered, which in turn affects local adaptation. In this study, I investigated how life history and genetic structure of freshwater salmonid would be modified by habitat fragmentation by comparing populations above and below a high dam. Results showed that the man-made reservoir had significantly increased migratory forms of white-spotted charr, which utilize abundant food resources in the reservoir. Stream residents dominated below the dam and showed significant genetic divergence with isolation-by-distance (IBD). However, no genetic divergence and IBD were observed among the populations above the reservoir. Assignment tests suggest that large migratory individuals had weak homing to their natal streams. Therefore, life history of white-spotted charr has been dramatically modified over the last 40 years, which also caused genetic homogeneity. The migratory behavior may be adaptive in terms of resource utilization but dispersal to non-natal streams might disrupt locally adapted genetic complexes.