Fertilization typically reduces ectomycorrhizal diversity shortly after its application but less is known about its longer-term influence on fungal species. Long-term effects are important in forests where fertilizer is rarely applied. We compared fungal species composition in western hemlock control plots with plots last fertilized 7 years ago with nitrogen (N) or nitrogen plus phosphorus (N + P). The N + P fertilization had a significant lingering effect, increasing the tree size and foliar P content of the western hemlocks. From ectomycorrhizal roots of 24-year-old trees from northern Vancouver Island, Canada, we identified fungi from 12 samples per treatment, by amplifying, cloning, and sequencing fungal ribosomal DNA fragments, placing sequences with 97% or more identity in the same operational taxonomic unit (OTU). Diversity was high across treatments; we detected 77 fungal OTUs, 52 from ectomycorrhizal genera, among 922 clone sequences. The five most frequent OTUs were similar in abundance across treatments. Only 19 OTUs matched any of the 197 previously reported ectomycorrhizal species of western hemlock. Species composition but not diversity in nitrogen plus phosphorus plots differed significantly from control or nitrogen plots. Two Cortinarius OTUs were indicator species for nitrogen plus phosphorus plots and presence of Cortinarius cinnamomeus was correlated with control or nitrogen plots. After 7 years, fertilization history had made no detectable difference in ectomycorrhizal fungal diversity, but long-lasting changes in environment resulting from fertilization had a lingering effect on fungal ectomycorrhizal species composition.