The disjunction of the mesic coniferous forests of the Pacific Northwest (PNW) has long been of interest to biogeographers, and several hypotheses have been posed to explain the disjunct distribution pattern. Analysis of intraspecific chloroplast DNA variation (1785 bp of matK and 400 bp of rpl16) in Salix melanopsis allows these hypotheses to be tested. Our study confirmed the existence of three genetic races (uncorrected sequence divergence ranged from 0.7-1.1%) within the species, which differ in distribution and ecology. The mesic race, associated with mesic coniferous forests, was the focus of this study. This race consists of two major lineages (uncorrected sequence divergence ranged up to 0.28%), one of which is associated with an apparent glacial refugium south of glaciation in the northern Rocky Mountains. The three haplotypes that comprise the first lineage are largely segregated into separate river canyons that comprise the “Greater Clearwater Refugium”. The other major lineage includes three haplotypes that occur throughout the PNW, except in the core of the Clearwater refugium. Vicariance is implicated in the origin of this latter lineage. Dispersal both before and during the Holocene appears to have occurred: the colonization of the Cascade Range from the Rocky Mountains, and later the dispersal of the Cascade haplotype into the area formerly buried by Cordilleran ice. More limited dispersal of Rocky Mountain haplotypes has resulted in contact zones with elevated haplotype diversity. The results of this study allow us to refine previous phylogeographic hypotheses of the PNW. Phylogenetic relationships within Salix sect. Longifoliae, the group that includes S. melanopsis, were also inferred. The sequence data produced phylogenetic hypotheses that were congruent with those obtained from an earlier analysis of cpDNA restriction site data.