Our study used allozyme analyses to evaluate potential impacts of ecological restoration treatments on genetic diversity of ponderosa pine (Pinus ponderosa var. scopulorum) populations within the Fort Valley Experimental Forest near Flagstaff, AZ. Allele frequencies varied among pre-settlement clumps, with trees more closely related to each other within clumps. This clumpy spatial stand structure typical of reference conditions thus represents "genetic neighborhoods" and suggests restoration of clumpy versus more evenly dispersed trees in naturally regenerating stands will protect evolutionary genetic patterns. Compared to pre-settlement populations, post-settlement trees had slightly greater heterozygosity, and allelic richness and allele frequencies varied between these two age groups. These genetic differences could have resulted from different selective conditions under which the two age groups became established. Genetic diversity of populations created using different selection criteria for residual post-settlement trees did not vary but simulated removal of 75% of post-settlement trees decreased allelic richness. Maintaining more clumps created from post-settlement populations with higher tree densities across the landscape would be more effective at conserving allelic richness. Overall results of this study indicate use of genetic structure and diversity can help guide restoration treatments to help ensure adaptive potential is conserved.