Whitebark pine is an important reforestation species in the northern Rocky Mountains for enhancement of wildlife habitat. Production of container-grown whitebark pine seedlings at the USDA Forest Service Nursery in Coeur d'Alene, Idaho has been increasing the past several years. Diseases continue to be an important limiting factor in seedling production. Recent evaluations implicated Fusarium solani and F. proliferatum as important pathogens of young germinants and seedlings. Both fungal species commonly contaminated whitebark pine seed prior to sowing. Pathogen spread during stratification resulted in very high levels of seed contamination. Fusarium spp. adversely affected seed germination as well as initiated high seedling disease levels. Not all seedlots were equally affected by diseases, even though most seeds were contaminated. Seedling vigor, probably related to seed germinative energy, may have been an important factor affecting disease severity. Efforts to reduce contamination by mechanical brushing or treatments with hydrogen peroxide or bleach solutions were ineffective. Seed-borne inoculum is important in disease epidemiology. Improved techniques to reduce level of pathogen contamination and spread during seed processing are required.