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Forestry in Sweden largely relies on planting genetically improved seedlings after clear-cutting, and high survival and early growth of planted seedlings is vital for stand establishment, economic viability, and carbon sequestration. Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) are the two most important tree species in Swedish forest stands and both are associated with a variety of ectomycorrhizal fungi. While seedlings are generally not fertilized at outplanting, previous results have shown that fertilization with arginine phosphate can increase root growth and seedling survival. However, it is not clear how this affects fungal community composition on the roots of growing seedlings. In a planting experiment sampled after one and two growing seasons, we found that planting position had the largest effects both on seedling performance and on fungal community composition and provide insight into the early stages of fungal community succession on planted Norway spruce and Scots pine seedlings. Fungal taxa present on seedlings before planting persisted on seedling roots, while some degree of novel colonization by site indigenous taxa was observed. Fertilization modified the relative abundance of some fungal taxa but did not lead to significant changes in overall community composition. In terms of seedling performance, ammonium nitrate led to increased mortality while arginine phosphate improved root growth.