Phylogeography is a field of science that uses genetics tools to understand how historical events have shaped the genetic diversity of species. The current natural ranges of 2 North American hard pines species, jack pine (Pinus banksiana Lamb.) and lodgepole pine (Pinus contorta Dougl. ex. Loud.), were almost completely covered by ice sheets during the last glacial maximum, 21,000 years ago. For this reason, these 2 species represent excellent models for studying the effect of the last glacial period on genetic diversity. Furthermore, they help provide a global image of colonization pathways used by species as the climate became warmer at the beginning of the Holocene. The use of DNA markers from chloroplast and mitochondrial genomes allowed detection of a geographical structure for each species. This structure results from landscape features that altered gene flow between sub-groups of populations, so favouring genetic differentiation between such groups during the glacial era. Natural introgression between the 2 species and fluctuations in their natural ranges that would have occurred during the Holocene, were also detected using the genetic tools developed. Historical, theoretical and methodological contexts are also presented to allow comparisons of these results with those from other species within the boreal ecosystem.