Summary Thirty‐one fungi, members of Ascomycota and Deuteromycota, were isolated from cones/seeds of 28 hosts (Pinus spp.) originating from East Asia, Europe and North America, and growing at the Montreal Botanical Garden, Canada. A total of 21 taxa of these isolated fungi are considered pathogens. The damage severity was most prevalent on Diploxylon pines of European provenance (Pinus nigra, Pinus mugo and Pinus sylvestris), and one indigenous North American species (Pinus albicaulis). Twelve fungi occurred on different hosts, i.e. Sphaeropsis sapinea (12), Herpotrichia juniperi (8), Truncatella hartigii (7), Ceuthospora sp. (5), Fusarium, spp. (5), Pestalotiopsis funerea (3), Phomopsis sp. (3), Valsa spp. (anamorph. Cytospora) (3), Diaporthe sp. (3), Fusicoccum sp. (2) and Sirococcus strobilinus (2). Sphaeropsis sapinea, Herpotrichia juniperi, Phomopsis conorum, Truncatella hartigii, Tubercularia sp. and Valsa spp. were related to high cone and seed damage. For the most frequently observed Sphaeropsis sapinea damage, the subgenus Haploxylon was less susceptible than Diploxylon, and P. sylvestris less than P. nigra and P. mugo. Pinus resinosa showed more tolerance to S. sapinea. Truncatella hartigii was more frequently associated with necrotic lesions on cones/seeds in comparison with Pestalotiopsis funerea. The results are discussed in the context of arboretum, seed orchard, nursery and quarantine management.