Maternally inherited mitochondrial DNA haplotypes in whitebark pine (Pinus albicaulis Engelm.) were used to examine the maternal genetic structure at three hierarchical spatial scales: fine scale, coarse scale, and interpopulation. These data were used to draw inferences into Clark’s nutcracker (Nucifraga columbiana Wilson) seedcaching flight distances. Statistical analyses of fine-scale and coarse-scale distribution of haplotypes showed no apparent signs of deviation from a random pattern. This suggests nutcrackers are effective in dispersal of seed within populations, which is consistent with data gathered on nutcracker seed-caching behavior. However, the lack of homogeneity in haplotype frequencies among populations indicates nutcrackers rarely disperse seeds across large gaps (>20 km) in subalpine habitat.