Forest management will protect genetic integrity of tree species only if their genetic diversity is understood and considered in decision-making. Genetic knowledge is particularly important for species such as ponderosa pine (Pinus ponderosa Dougl. ex Laws.) that are distributed across wide geographic distances and types of climates. A ponderosa pine study initiated in 1910 at the Fort Valley Experimental Forest is among the earliest ponderosa pine genetic research efforts in the United States. This study contributed to the description of ponderosa pine's varietal differences, genetic diversity and adaptation patterns, and helped confirm the importance of using local seed sources. The role this and other pioneer studies had in improving forest management of ponderosa pine was, and still is critical. These early studies have long-term value because they improve our knowledge of responses to climate change and our understanding of genetic variability in physiology and pest resistance in older trees. More recently, studies of natural ponderosa pine stands at Fort Valley using molecular markers have shown the importance of stand structure and disturbance regimes to genetic composition and structural patterns. This knowledge is important to ensure ecological restoration efforts in ponderosa pine forests will also restore and protect genetic integrity into the future. Highlights of these historical and contemporary studies at Fort Valley are summarized and their applications to management of ponderosa pine forests are described.