Analysis of "neutral" molecular markers and "adaptive" quantitative traits are common methods of assessing genetic diversity and population structure. Molecular markers typically reflect the effects of demographic and stochastic processes but are generally assumed to not reflect natural selection. Conversely, quantitative (or "adaptive") traits can be associated with climatic or other environmental variables that drive natural selection, but may not reflect the past demographic processes, such as bottlenecks, post-glacial recolonization, and population isolation. The genetics of whitebark pine has been studied using both molecular markers and adaptive traits, but never from a common set of samples so that the results could be directly compared. In addition, previous studies have not included samples from the Olympic Mountains in northwestern Washington, the westernmost distribution of whitebark pine that is geographically isolated from the rest of the species range.