To what degree are patterns of genetic structure in fragmented systems the result of contemporary landscape versus history? We examined the distribution of genetic diversity as a function of colonization history and contemporary landscape in four fish species inhabiting a hierarchically fragmented, unaltered system, the Kogaluk drainage (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 was examined regardless of the generations since their arrival. Approximate Bayesian computation (ABC) analyses suggest colonization took place from the southwest. The species exhibit similar diversity patterns despite different [Formula: see text] values and generation intervals. Contemporary gene flow was largely negligible except for gene flow from a centrally located lake. These results suggest landscape has driven colonization history, which still has influence on genetic structuring. The species are widespread. Understanding how they behave in the pristine Kogaluk provides a baseline against which to evaluate how other anthropogenically perturbed systems are performing. Improved understanding of historical and contemporary processes is required to fully explain diversity patterns in complex metapopulations.