A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we used whole-genome re-sequencing data from three related Populus species to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, population-scaled recombination rate and linkage disequilibrium. Our analyses revealed that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Consistent with this, linkage disequilibrium decay was fastest in P. tremuloides and slowest in P. trichocarpa. Pervasive natural selection has been proven to be the primary force creating significant positive correlations between neutral polymorphism and recombination rate in all three species. Disparate effective population sizes and recombination rates among species, on the other hand, drive the distinct magnitudes and signatures of linked selection and consequent heterogeneous patterns of genomic variation among them. We find that purifying selection against slightly deleterious non-synonymous mutations is more effective in regions experiencing high recombination, which may provide one explanation for a partially positive association between recombination rate and gene density in these species. Moreover, distinct signatures of linked selection dependent on gene density are found between genic and intergenic regions within each species. To our knowledge, the present work is the first comparative population genomic study among forest tree species and represents an important step toward dissecting how the interactions of various evolutionary forces have shaped genomic variation within and among these ecologically and economically important tree species.