I evaluated the relative importance of contemporary and historical factors on the spatial population genetic structure of brook trout ('Salvelinus fontinalis') within and around Gros Morne National Park, Newfoundland. I studied 13 populations of brook trout using five microsatellite loci thought to be linked to quantitative trait loci (QTL) for body size and/or upper thermal tolerance and four loci not known to be linked to such QTL. Putative historical landscape features and contemporary barriers explained most of the genetic variation observed in the study area. QTL-linked and non QTL-linked markers led to contrasting patterns of population structure but differences in levels of intra-population diversity, rather than selection, appeared sufficient to explain observed differences among markers. This study provides important insights on the evolution of nonequilibrium population structure in areas affected by landscape rearrangement and represents one of the first attempts to infer selection in natural populations using QTL information.