Healthy-appearing 1-0 ponderosa and lodgepole pine seedlings were assayed for root infection and colonization by potentially-pathogenic fungi following pre-sowing soil treatments which included methyl bromide/chloropicrin (MBC) fumigation, fallowing with or/without periodic cultivation, and amending soil with mushroom composts or undecomposed sawdust. Levels of root colonization by Fusarium spp. on both conifer species were lowest in MBC-treated fields. Fallowing, particularly without cultivation, was nearly as beneficial in reducing Fusarium root colonization for lodgepole pine seedlings. These results correlated well with 2-0 seedling densities in treated fields. Fusarium oxysporum was the most common colonizer of roots of healthy seedlings as well as the most important cause of seedling disease. Continued efforts are underway to develop satisfactory alternatives to MBC fumigation at the Lucky Peak Nursery.