To what degree are patterns of observed genetic diversity and differentiation in spatially fragmented systems the result of contemporary landscape features vs. historical processes? We addressed this question by examining the spatial distribution of genetic diversity as a function of colonization history and contemporary landscape in four fish species inhabiting a hierarchically structured and spatially fragmented system that is largely free of anthropogenic influence, the Kogaluk river drainage in Labrador: lake trout (Salvelinus namaycush), longnose sucker (Catostomus catostomus), round whitefish (Prosopium cylindraceum), and lake chub (Couesius plumbeus). The footprint of colonization history was still observable in the three species where this issue could be examined regardless of the number of generations that elapsed since their estimated arrival to the area. ABC analyses for all three species suggest colonization took place from the southwest. All species exhibit similar diversity patterns despite their different N ̂_e s and generation intervals. Contemporary gene flow was largely negligible across all four species with the exception of gene flow up- and downstream from a centrally located lake. These results suggest landscape has driven colonization history, which still has a major influence on the genetic structuring across all four species. The four species examined are widespread throughout Canada. Understanding how they behave in the Kogaluk drainage, a drainagewhich is free of direct anthropogenic interference provides a baseline against which to evaluate how other systems undergoing anthropogenic perturbations are performing. We conclude that an improved understanding of historical and contemporary processes is required to fully explain observed patterns of structure and gene flow in spatially complex metapopulation systems.