Identifying the factors controlling tree mortality is key to understanding the effects of ongoing global change on treeline movement and species composition. One potentially significant but little studied factor that impacts the formation of treelines is mortality caused by snow fungi. We studied the mortality patterns of Pinus cembra, a typical treeline species of the Central Alps of Switzerland, in two plantations located on opposite slopes of the Dischma valley (Northeast [NE] and Southwest [SW]) above the current treeline. In 1975, 33,000 P. cembra trees were planted at the NE site and 550 trees at the smaller SW site. All trees have been periodically monitored for survival since then. After 30 years, only ca. 5% of all P. cembra trees survived in both plantations. Two species of pathogenic snow fungus, Gremmeniella abietina and Phacidium. infestans, were major mortality agents for saplings. High rates of infection by Gremmeniella corresponded to late snowmelt and high ratios of rainfall to temperature. High rates of infection by Phacidium corresponded to earlier snowmelt and were spatially associated with P. cembra mature trees that had been present in the area before the time of planting. We provide experimental evidence that snow fungi are a primary cause of sapling tree mortality at treeline. Although additional evidence from different geographic regions and more natural treeline distributions is needed, our results suggest that the prevalence of snow fungi may prevent establishment of trees above the current treeline at present, and under future climate scenarios.